34 results on '"Pak-Kei Chan"'
Search Results
2. BioID data of c-MYC interacting protein partners in cultured cells and xenograft tumors
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Pak-Kei Chan, Tharan Srikumar, Dharmendra Dingar, Manpreet Kalkat, Linda Z. Penn, and Brian Raught
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Science (General) ,Q1-390 - Abstract
BioID was performed using FlagBirA⁎ (the R118G biotin ligase mutant protein) and FlagBirA⁎-Myc in HEK293 T-REx cells maintained both under standard cell culture conditions and as mouse xenografts. The mass spectrometry dataset acquired in this study has been uploaded to the MassIVE repository with ID: MSV000078518, and consists of 28 ⁎.raw MS files acquired on an Orbitrap Velos instrument, collected in data-dependent mode. iProphet processed MS/MS search results are also included as a reference. This study has been published as “BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors”, by Dingar et al. in the Journal of Proteomics, 2014 [1].
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- 2014
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3. Identification of c-MYC SUMOylation by mass spectrometry.
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Manpreet Kalkat, Pak-Kei Chan, Amanda R Wasylishen, Tharan Srikumar, Sam S Kim, Romina Ponzielli, David P Bazett-Jones, Brian Raught, and Linda Z Penn
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Medicine ,Science - 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. This deregulation can take many forms, including altered post-translational regulation. 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 two 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.
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- 2014
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4. Supplementary Table 5 from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity
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Linda Z. Penn, Paul C. Boutros, Brian Raught, Natalie Meyer, Ling Huang, Peter J. Mullen, Pak-Kei Chan, Manpreet Kalkat, William B. Tu, Dharmendra Dingar, Christina Bros, Michelle Chan-Seng-Yue, and Amanda R. Wasylishen
- Abstract
XLSX file, 14K, Gene expression changes common to wild type MYC and all phosphorylation mutants (112 genes).
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- 2023
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5. Supplementary Table 4 from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity
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Linda Z. Penn, Paul C. Boutros, Brian Raught, Natalie Meyer, Ling Huang, Peter J. Mullen, Pak-Kei Chan, Manpreet Kalkat, William B. Tu, Dharmendra Dingar, Christina Bros, Michelle Chan-Seng-Yue, and Amanda R. Wasylishen
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XLS file, 160K, GO Analysis of significant genes expression changes.
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- 2023
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6. Supplementary Table 6 from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity
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Linda Z. Penn, Paul C. Boutros, Brian Raught, Natalie Meyer, Ling Huang, Peter J. Mullen, Pak-Kei Chan, Manpreet Kalkat, William B. Tu, Dharmendra Dingar, Christina Bros, Michelle Chan-Seng-Yue, and Amanda R. Wasylishen
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XLS file, 403K, Expression comparison between wild-type MYC and MYC phosphorylation mutants (from Venn diagram)
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- 2023
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7. Supplementary Table 2 from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity
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Linda Z. Penn, Paul C. Boutros, Brian Raught, Natalie Meyer, Ling Huang, Peter J. Mullen, Pak-Kei Chan, Manpreet Kalkat, William B. Tu, Dharmendra Dingar, Christina Bros, Michelle Chan-Seng-Yue, and Amanda R. Wasylishen
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XLS file, 2439K, MYC ChIP-on-chip data in MCF10A cells.
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- 2023
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8. Supplementary Table 1 from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity
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Linda Z. Penn, Paul C. Boutros, Brian Raught, Natalie Meyer, Ling Huang, Peter J. Mullen, Pak-Kei Chan, Manpreet Kalkat, William B. Tu, Dharmendra Dingar, Christina Bros, Michelle Chan-Seng-Yue, and Amanda R. Wasylishen
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XLS file, 14K, Phosphopeptide analysis for ectopic MYC in 293Tv cells.
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- 2023
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9. Supplementary Table 9 from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity
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Linda Z. Penn, Paul C. Boutros, Brian Raught, Natalie Meyer, Ling Huang, Peter J. Mullen, Pak-Kei Chan, Manpreet Kalkat, William B. Tu, Dharmendra Dingar, Christina Bros, Michelle Chan-Seng-Yue, and Amanda R. Wasylishen
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XLS file, 98K, GO analysis of common gene expression changes.
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- 2023
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10. Supplementary Materials and Methods from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity
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Linda Z. Penn, Paul C. Boutros, Brian Raught, Natalie Meyer, Ling Huang, Peter J. Mullen, Pak-Kei Chan, Manpreet Kalkat, William B. Tu, Dharmendra Dingar, Christina Bros, Michelle Chan-Seng-Yue, and Amanda R. Wasylishen
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PDF file, 136K.
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- 2023
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11. Supplementary Table 3 from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity
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Linda Z. Penn, Paul C. Boutros, Brian Raught, Natalie Meyer, Ling Huang, Peter J. Mullen, Pak-Kei Chan, Manpreet Kalkat, William B. Tu, Dharmendra Dingar, Christina Bros, Michelle Chan-Seng-Yue, and Amanda R. Wasylishen
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XLS file, 319K, Expression array analysis of MCF10A 3D cultures at 4 days.
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- 2023
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12. Supplementary Table 8 from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity
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Linda Z. Penn, Paul C. Boutros, Brian Raught, Natalie Meyer, Ling Huang, Peter J. Mullen, Pak-Kei Chan, Manpreet Kalkat, William B. Tu, Dharmendra Dingar, Christina Bros, Michelle Chan-Seng-Yue, and Amanda R. Wasylishen
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XLS file, 3148K, Compiled expression array and ChIP-on-chip data.
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- 2023
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13. Supplementary Table 7 from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity
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Linda Z. Penn, Paul C. Boutros, Brian Raught, Natalie Meyer, Ling Huang, Peter J. Mullen, Pak-Kei Chan, Manpreet Kalkat, William B. Tu, Dharmendra Dingar, Christina Bros, Michelle Chan-Seng-Yue, and Amanda R. Wasylishen
- Abstract
XLSX file, 16K, Gene expression changes common to all gain-of-function MYC phosphorylation mutants (158 genes).
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- 2023
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14. Supplementary Figures from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity
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Linda Z. Penn, Paul C. Boutros, Brian Raught, Natalie Meyer, Ling Huang, Peter J. Mullen, Pak-Kei Chan, Manpreet Kalkat, William B. Tu, Dharmendra Dingar, Christina Bros, Michelle Chan-Seng-Yue, and Amanda R. Wasylishen
- Abstract
PDF file, 498K, Supplementary Figures S1-6 Supplementary Figure S1: Phosphorylation mutants increase Myc-induced transformation in MCF10A cells. Supplementary Figure S2: Phosphorylation mutants increase Myc-induced transformation in SH-EP cells. Supplementary Figure S3: Phosphorylation mutants do not effect MYC protein stability. Supplementary Figure S4: Serum starvation of MCF10A-GFP and MCF10A-MYC cells. Supplementary Figure S5: MYC protein expression through morphogenesis of MCF10A cells in 3D culture. Supplementary Figure S6: Characterization of day 4 acini for mRNA expression array analysis.
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- 2023
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15. Improving the performance of neural networks in classification using fuzzy linear regression.
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Chun Hung Cheng 0001, Boon Toh Low, Pak-Kei Chan, and Jaideep Motwani
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- 2001
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16. Mannich reactions in room temperature ionic liquids (RTILs): An advanced undergraduate project of green chemistry and structural elucidation
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Kendrew K.W. Mak, Jane Siu, Y.M. Lai, and Pak-kei Chan
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Ionic solutions -- Chemical properties ,Pyridine -- Chemical properties ,Imidazole -- Chemical properties ,Sciences education ,Chemistry ,Education ,Science and technology - Abstract
An advanced elective laboratory course is offered in order to help students leap the gap between undergraduate laboratory experience and the independent working environment in post graduate studies. The synthesis of room temperature ionic liquids and their application to Mannich reactions is a project-based experiment developed to be a part of advanced program which provides a opportunity for students to experience innovative ideas in chemical research.
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- 2006
17. MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation
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Angelina Stojanova, Pak-Kei Chan, Linda Z. Penn, Fereshteh Khosravi, Brian Raught, William B. Tu, Paul C. Boutros, Max Kotlyar, Igor Jurisica, and Romina Ponzielli
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0301 basic medicine ,Transcription, Genetic ,Amino Acid Motifs ,SWI/SNF complex/BAF complex ,Basic helix-loop-helix leucine zipper transcription factors ,Cell Transformation ,Repetitive Sequences ,protein-protein interaction ,transcriptional regulation ,Proto-Oncogene Proteins c-myc ,SMARCB1 ,Conserved Sequence ,Tumor ,cellular transformation ,Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ,SMARCB1 Protein ,SWI/SNF ,Chromatin ,Cell biology ,Gene Expression Regulation, Neoplastic ,Amino Acid ,c-MYC ,Cell Transformation, Neoplastic ,chromatin regulatory complex ,Transcription ,MAX ,Protein Binding ,Repetitive Sequences, Amino Acid ,Leucine zipper ,rhabdoid tumors ,Biology ,Chromatin remodeling ,Cell Line ,03 medical and health sciences ,Genetic ,Cell Line, Tumor ,INI1/SMARCB1/hSNF5/BAF47 ,Humans ,Molecular Biology ,Cell Proliferation ,Neoplastic ,Leucine Zippers ,SWI/SNF complex ,Cell Biology ,Chromatin Assembly and Disassembly ,Molecular biology ,HEK293 Cells ,030104 developmental biology ,Gene Expression Regulation ,Biochemistry and Cell Biology ,Protein Multimerization ,Reports ,Developmental Biology - 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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- 2016
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18. MYC dephosphorylation by the PP1/PNUTS phosphatase complex regulates chromatin binding and protein stability
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Kathleen E. Houlahan, William B. Tu, Jason De Melo, Aaliya Tamachi, Paul C. Boutros, Dharmendra Dingar, Diana Resetca, Linda Z. Penn, Manpreet Kalkat, Corey Lourenco, Brian Raught, and Pak-Kei Chan
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0301 basic medicine ,Electrophoresis ,Chromatin Immunoprecipitation ,Immunoprecipitation ,Science ,Phosphatase ,Immunoblotting ,General Physics and Astronomy ,Hyperphosphorylation ,General Biochemistry, Genetics and Molecular Biology ,Article ,Mass Spectrometry ,Cell Line ,Proto-Oncogene Proteins c-myc ,03 medical and health sciences ,Rare Diseases ,Cell Line, Tumor ,Protein Phosphatase 1 ,Genetics ,2.1 Biological and endogenous factors ,Humans ,Electrophoresis, Gel, Two-Dimensional ,Aetiology ,lcsh:Science ,Cancer ,Gel ,Multidisciplinary ,Tumor ,Chemistry ,Protein Stability ,Chromatin binding ,Nuclear Proteins ,RNA-Binding Proteins ,Protein phosphatase 1 ,General Chemistry ,Chromatin ,3. Good health ,Cell biology ,DNA-Binding Proteins ,030104 developmental biology ,Generic Health Relevance ,Two-Dimensional ,Phosphatase complex ,lcsh:Q ,Chromatin immunoprecipitation ,Biotechnology - 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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- 2018
19. The SUMO-specific isopeptidase SENP2 associates dynamically with nuclear pore complexes through interactions with karyopherins and the Nup107-160 nucleoporin subcomplex
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Pak Kei Chan, Michael J. Matunis, Jacqueline Goeres, Brian Raught, Hong Zhang, and Debaditya Mukhopadhyay
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SUMO-1 Protein ,Amino Acid Motifs ,Nuclear Localization Signals ,Active Transport, Cell Nucleus ,Karyopherins ,Biology ,03 medical and health sciences ,0302 clinical medicine ,Humans ,Nuclear pore ,Nuclear protein ,Nuclear export signal ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,Nuclear Functions ,HEK 293 cells ,Nuclear Proteins ,Articles ,Cell Biology ,Protein Structure, Tertiary ,Cell biology ,Nuclear Pore Complex Proteins ,Cysteine Endopeptidases ,HEK293 Cells ,Biochemistry ,Multiprotein Complexes ,030220 oncology & carcinogenesis ,Nuclear Pore ,Nucleoporin ,Nuclear transport ,HeLa Cells - Abstract
We determined that the small, ubiquitin-related modifier–specific isopeptidase, SENP2, is dynamically associated with nuclear pore complexes (NPCs). This association is determined by the activities of three N-terminal signals in SENP2: a high-affinity nuclear localization sequence, an Nup107-160–binding element, and a nuclear export signal. NPC association, and its potential regulation, affects SENP2 accessibility to substrates., The association of small, ubiquitin-related modifier–specific isopeptidases (also known as sentrin-specific proteases, or SENPs) with nuclear pore complexes (NPCs) is conserved in eukaryotic organisms ranging from yeast to mammals. However, the functional significance of this association remains poorly understood, particularly in mammalian cells. In this study, we have characterized the molecular basis for interactions between SENP2 and NPCs in human cells. Using fluorescence recovery after photobleaching, we demonstrate that SENP2, although concentrated at the nuclear basket, is dynamically associated with NPCs. This association is mediated by multiple targeting elements within the N-terminus of SENP2 that function cooperatively to mediate NPC localization. One of these elements consists of a high-affinity nuclear localization signal that mediates indirect tethering to FG-repeat–containing nucleoporins through karyopherins. A second element mediates interactions with the Nup107-160 nucleoporin subcomplex. A third element consists of a nuclear export signal. Collectively, our findings reveal that SENP2 is tethered to NPCs through a complex interplay of interactions with nuclear import and export receptors and nucleoporins. Disruption of these interactions enhances SENP2 substrate accessibility, suggesting an important regulatory node in the SUMO pathway.
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- 2011
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20. BioID data of c-MYC interacting protein partners in cultured cells and xenograft tumors
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Linda Z. Penn, Manpreet Kalkat, Dharmendra Dingar, Pak-Kei Chan, Tharan Srikumar, and Brian Raught
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chemistry.chemical_classification ,DNA ligase ,Multidisciplinary ,business.industry ,HEK 293 cells ,Orbitrap ,Proteomics ,Bioinformatics ,lcsh:Computer applications to medicine. Medical informatics ,Molecular biology ,law.invention ,chemistry.chemical_compound ,Biotin ,chemistry ,Mutant protein ,law ,Medicine ,lcsh:R858-859.7 ,business ,lcsh:Science (General) ,Tumor xenograft ,Data Article ,lcsh:Q1-390 - Abstract
BioID was performed using FlagBirA⁎ (the R118G biotin ligase mutant protein) and FlagBirA⁎-Myc in HEK293 T-REx cells maintained both under standard cell culture conditions and as mouse xenografts. The mass spectrometry dataset acquired in this study has been uploaded to the MassIVE repository with ID: MSV000078518, and consists of 28 ⁎.raw MS files acquired on an Orbitrap Velos instrument, collected in data-dependent mode. iProphet processed MS/MS search results are also included as a reference. This study has been published as “BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors”, by Dingar et al. in the Journal of Proteomics, 2014 [1].
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- 2014
21. MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis
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Yong Wei, Brian Raught, Manpreet Kalkat, Maria Sunnerhagen, Pak-Kei Chan, Corey Lourenco, Diana Resetca, Susan J. Done, Linda Z. Penn, Paul C. Boutros, Yufeng Tong, Natasha Vitkin, and Yu-Jia Shiah
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0301 basic medicine ,Breast Neoplasms ,Interactome ,Protein–protein interaction ,Proto-Oncogene Proteins c-myc ,Mice ,Transcription Factors, TFII ,03 medical and health sciences ,Protein Domains ,Mice, Inbred NOD ,Cell Line, Tumor ,Protein Interaction Mapping ,Animals ,Humans ,Protein Isoforms ,Molecular Biology ,Transcription factor ,biology ,General transcription factor ,Gene Expression Profiling ,Cell Biology ,Survival Analysis ,Xenograft Model Antitumor Assays ,Phenotype ,Tumor Burden ,Cell biology ,Gene Expression Regulation, Neoplastic ,Cell Transformation, Neoplastic ,HEK293 Cells ,030104 developmental biology ,Histone ,Acetylation ,biology.protein ,Female ,Transcription factor II F ,Protein Binding ,Signal Transduction - 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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- 2018
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22. Identification of c-MYC SUMOylation by Mass Spectrometry
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David P. Bazett-Jones, Romina Ponzielli, Pak Kei Chan, Sam S. Kim, Amanda R. Wasylishen, Brian Raught, Linda Z. Penn, Manpreet Kalkat, and Tharan Srikumar
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Programmed cell death ,Immunoprecipitation ,Cell ,SUMO protein ,lcsh:Medicine ,Biology ,Arginine ,Mass Spectrometry ,Proto-Oncogene Proteins c-myc ,Molecular Cell Biology ,Transcriptional regulation ,medicine ,Humans ,lcsh:Science ,Transcription factor ,Molecular Biology ,Multidisciplinary ,Oncogene ,HEK 293 cells ,lcsh:R ,Biology and Life Sciences ,Sumoylation ,Cell Biology ,Molecular biology ,Cell biology ,medicine.anatomical_structure ,HEK293 Cells ,Amino Acid Substitution ,MCF-7 Cells ,lcsh:Q ,Research Article - 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. This deregulation can take many forms, including altered post-translational regulation. 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 two 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.
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- 2014
23. BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors
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Brian Raught, Linda Z. Penn, Igor Jurisica, Pak-Kei Chan, William B. Tu, Manpreet Kalkat, Dharmendra Dingar, Max Kolyar, Etienne Coyaud, Mathieu Lupien, Swneke D. Bailey, Romina Ponzielli, Tharan Srikumar, and Annie Huang
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Male ,Chromosomal Proteins, Non-Histone ,Two-hybrid screening ,Biophysics ,Computational biology ,Mice, SCID ,Biology ,Proteomics ,Biochemistry ,Interactome ,Chromatin remodeling ,Lysine Acetyltransferase 5 ,Chromodomain ,Proto-Oncogene Proteins c-myc ,Mice ,Mice, Inbred NOD ,Cell Line, Tumor ,Animals ,Humans ,KAT5 ,Transcription factor ,Histone Acetyltransferases ,Genetics ,Oncogene ,Neoplasms, Experimental ,DNA-Binding Proteins ,Heterografts ,Neoplasm Transplantation ,Transcription Factors - Abstract
The BioID proximity-based biotin labeling technique was recently developed for the characterization of protein–protein interaction networks [1]. 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 c-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. Putative novel MYC interactors include components of the STAGA/KAT5 and SWI/SNF chromatin remodeling complexes, DNA repair and replication factors, general transcription and elongation factors, and transcriptional co-regulators such as the DNA helicase protein 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 MYC–CHD8 interaction using both a yeast two hybrid analysis and the proximity-based ligation assay. In sum, we demonstrate that BioID can be utilized to identify bona fide interacting partners for a chromatin-associated protein in vivo . This technique will allow for a much improved understanding of protein–protein interactions in a previously inaccessible biological setting. Biological significance The c- MYC ( MYC ) oncogene is a transcription factor that plays important roles in cancer initiation and progression. MYC expression is deregulated in more than 50% of human cancers, but the role of this protein in normal cell biology and tumor progression is still not well understood, in part because identifying MYC-interacting proteins has been technically challenging: MYC-containing chromatin-associated complexes are difficult to isolate using traditional affinity purification methods, and the MYC protein is exceptionally labile, with a half-life of only ~ 30 min. Developing a new strategy to gain insight into MYC-containing protein complexes would thus mark a key advance in cancer research. The recently described BioID proximity-based labeling technique represents a promising new complementary approach for the characterization of protein–protein interactions (PPIs) in cultured cells. Here we report that BioID can also be used to characterize protein–protein interactions for a chromatin-associated protein in tumor xenografts, and present a comprehensive, high confidence in vivo MYC interactome. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.
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- 2014
24. MYC phosphorylation at novel regulatory regions suppresses transforming activity
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Natalie Meyer, Peter J. Mullen, Christina Bros, Amanda R. Wasylishen, Michelle Chan-Seng-Yue, Pak Kei Chan, Ling Huang, Linda Z. Penn, Paul C. Boutros, William B. Tu, Brian Raught, Dharmendra Dingar, and Manpreet Kalkat
- Subjects
Cancer Research ,Chromatin Immunoprecipitation ,Mutant ,Blotting, Western ,Apoptosis ,Biology ,Regulatory Sequences, Nucleic Acid ,medicine.disease_cause ,Real-Time Polymerase Chain Reaction ,Colony-Forming Units Assay ,Proto-Oncogene Proteins c-myc ,Neuroblastoma ,Oxygen Consumption ,medicine ,Biomarkers, Tumor ,Cell Adhesion ,Humans ,RNA, Messenger ,Phosphorylation ,Mammary Glands, Human ,Gene ,Cells, Cultured ,Cell Proliferation ,Oligonucleotide Array Sequence Analysis ,Regulation of gene expression ,Reverse Transcriptase Polymerase Chain Reaction ,Gene Expression Profiling ,Epithelial Cells ,Gene expression profiling ,Gene Expression Regulation, Neoplastic ,Cell Transformation, Neoplastic ,Oncology ,Regulatory sequence ,Mutation ,Cancer research ,Female ,Carcinogenesis ,Chromatin immunoprecipitation - Abstract
Despite its central role in human cancer, MYC deregulation is insufficient by itself to transform cells. Because inherent mechanisms of neoplastic control prevent precancerous lesions from becoming fully malignant, identifying transforming alleles of MYC that bypass such controls may provide fundamental insights into tumorigenesis. To date, the only activated allele of MYC known is T58A, the study of which led to identification of the tumor suppressor FBXW7 and its regulator USP28 as a novel therapeutic target. In this study, we screened a panel of MYC phosphorylation mutants for their ability to promote anchorage-independent colony growth of human MCF10A mammary epithelial cells, identifying S71A/S81A and T343A/S344A/S347A/S348A as more potent oncogenic mutants compared with wild-type (WT) MYC. The increased cell-transforming activity of these mutants was confirmed in SH-EP neuroblastoma cells and in three-dimensional MCF10A acini. Mechanistic investigations initiated by a genome-wide mRNA expression analysis of MCF10A acini identified 158 genes regulated by the mutant MYC alleles, compared with only 112 genes regulated by both WT and mutant alleles. Transcriptional gain-of-function was a common feature of the mutant alleles, with many additional genes uniquely dysregulated by individual mutant. Our work identifies novel sites of negative regulation in MYC and thus new sites for its therapeutic attack. Cancer Res; 73(21); 6504–15. ©2013 AACR.
- Published
- 2013
25. A strategy for modulation of enzymes in the ubiquitin system
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Elton Zeqiraj, Laurence Pelletier, Jason Moffat, Sirano Dhe-Paganon, Avinash Persaud, Konstantina Karamboulas, Michael Moran, Pak-Kei Chan, Dante Neculai, Philipp Alberts, Yanling Zhao, Andrew Vorobyov, Daniel Durocher, John R. Walker, Daniela Rotin, Brian Raught, Andreas Ernst, George V. Avvakumov, Abdellah Allali-Hassani, Masoud Vedadi, Pankaj Garg, Yu Chi Juang, Marie-Claude Landry, Linda G. Beatty, Christina Yeh, Ana-Mirela Neculai, Mike Tyers, Yihui Fan, Jiefei Tong, Frank Sicheri, Sachdev S. Sidhu, and Jianhua Yang
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Protein Conformation ,Ubiquitin-Protein Ligases ,Molecular Sequence Data ,SUMO enzymes ,Ubiquitin-conjugating enzyme ,Protein Structure, Secondary ,Article ,Deubiquitinating enzyme ,Small Molecule Libraries ,Protein structure ,Ubiquitin ,Endopeptidases ,Combinatorial Chemistry Techniques ,Humans ,Protease Inhibitors ,Amino Acid Sequence ,Conserved Sequence ,Multidisciplinary ,biology ,Ubiquitination ,Ubiquitin ligase ,HEK293 Cells ,Biochemistry ,Drug Design ,Ubiquitin-Conjugating Enzymes ,biology.protein ,Ubiquitin Thiolesterase ,Function (biology) - Abstract
Modifying Deubiquitinases Protein ubiquitination is a widespread mechanism for cellular regulation, and new regulators are valuable research tools and may help to generate therapeutic small molecules. Ernst et al. (p. 590 , published online 3 January) used known crystal structures to roughly define the interaction domain between a ubiquitin-specific protease and a ubiquitinated substrate and then screened ubiquitin variants with changes in these residues to find variants that acted as potent and specific regulators that could modify ubiquitin pathway regulation in cells.
- Published
- 2013
26. Proteomic profiling of the human cytomegalovirus UL35 gene products reveals a role for UL35 in the DNA repair response
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Brian Raught, Jayme Salsman, Madhav Jagannathan, Patrick Paladino, Graham Dellaire, Lori Frappier, and Pak-Kei Chan
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Gene Expression Regulation, Viral ,Proteomics ,DNA Repair ,DNA damage ,DNA repair ,Ubiquitin-Protein Ligases ,Immunology ,Cytomegalovirus ,Protein Serine-Threonine Kinases ,Microbiology ,Cell Line ,Ubiquitin-Specific Peptidase 7 ,DDB1 ,Viral Proteins ,Ubiquitin ,Virology ,Humans ,Gene ,Regulation of gene expression ,biology ,Cell Cycle ,Cell cycle ,Molecular biology ,Ubiquitin ligase ,Virus-Cell Interactions ,Insect Science ,Cytomegalovirus Infections ,Host-Pathogen Interactions ,biology.protein ,Carrier Proteins ,Ubiquitin Thiolesterase ,Protein Binding - Abstract
Human cytomegalovirus infections involve the extensive modification of host cell pathways, including cell cycle control, the regulation of the DNA damage response, and averting promyelocytic leukemia (PML)-mediated antiviral responses. The UL35 gene from human cytomegalovirus is important for viral gene expression and efficient replication and encodes two proteins, UL35 and UL35a, whose mechanism of action is not well understood. Here, affinity purification coupled with mass spectrometry was used to identify previously unknown human cellular targets of UL35 and UL35a. We demonstrate that both viral proteins interact with the ubiquitin-specific protease USP7, and that UL35 expression can alter USP7 subcellular localization. In addition, UL35 (but not UL35a) was found to associate with three components of the Cul4 DCAF1 E3 ubiquitin ligase complex (DCAF1, DDB1, and DDA1) previously shown to be targeted by the HIV-1 Vpr protein. The coimmunoprecipitation and immunofluorescence microscopy of DCAF1 mutants revealed that the C-terminal region of DCAF1 is required for association with UL35 and mediates the dramatic relocalization of DCAF1 to UL35 nuclear bodies, which also contain conjugated ubiquitin. As previously reported for the Vpr-DCAF1 interaction, UL35 (but not UL35a) expression resulted in the accumulation of cells in the G 2 phase of the cell cycle, which is typical of a DNA damage response, and activated the G 2 checkpoint in a DCAF1-dependent manner. In addition, UL35 (but not UL35a) induced γ-H2AX and 53BP1 foci, indicating the activation of DNA damage and repair responses. Therefore, the identified interactions suggest that UL35 can contribute to viral replication through the manipulation of host responses.
- Published
- 2011
27. MYC activity is negatively regulated by a C-terminal lysine cluster
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Aleksandra A. Pandyra, E. Sedivy, Manpreet Kalkat, Sam S. Kim, S. Oliveri, D. Konforte, Linda Z. Penn, Brian Raught, Christina Bros, Amanda R. Wasylishen, and Pak Kei Chan
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Cancer Research ,Mutant ,Genes, myc ,medicine.disease_cause ,Ubiquitin ,Transcription (biology) ,Neoplasms ,Genetics ,medicine ,Animals ,Humans ,Phosphorylation ,Molecular Biology ,Oncogene ,biology ,Protein Stability ,Lysine ,Cell cycle ,Molecular biology ,Rats ,Gene Expression Regulation ,Acetylation ,biology.protein ,Heterografts ,Carcinogenesis ,Cell Division - Abstract
The MYC oncogene is not only deregulated in cancer through abnormally high levels of expression, but also through oncogenic lesions in upstream signalling cascades. Modelling MYC deregulation using signalling mutants is a productive research strategy. For example, the MYC threonine-58 to alanine substitution mutant (T58A) within MYC-homology box 1 is more transforming than wild-type (WT) MYC, because of decreased apoptosis and increased protein stability. Understanding the regulatory mechanisms controlling T58 phosphorylation has led to new approaches for the development of MYC inhibitors. In this manuscript, we have extensively characterized a MYC signalling mutant in which six lysine residues near the highly conserved MYC homology box IV and basic region have been substituted to arginines (6KR). Previous literature suggests these lysines can undergo both ubiquitylation and acetylation. We show MYC 6KR is able to fully rescue the slow growth phenotype of HO15.19 MYC-null fibroblasts, and promote cell cycle entry of serum-starved MCF10A cells. Remarkably, 6KR increased anchorage-independent colony growth compared with WT MYC in both SH-EP and MCF10A cells. Moreover, it was also more potent in promoting xenograft tumour growth of Rat1A and SH-EP cells. Combined, our data identify this region and these six lysines as important residues for the negative regulation of MYC-induced transformation. Mechanistically, we demonstrate that, unlike T58A, the increased transformation is not a result of increased protein stability or a reduced capacity for 6KR to induce apoptosis. Through expression analysis and luciferase reporter assays, we show that 6KR has increased transcriptional activity compared with WT MYC. Combined, through a comprehensive evaluation across multiple cell types, we identify an important regulatory region within MYC. A better understanding of the full scope of signalling through these residues will provide further insights into the mechanisms contributing to MYC-induced tumorigenesis and may unveil novel therapeutic strategies to target Myc in cancer.
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- 2011
28. Abstract A08: Identification of c-MYC SUMOylation by mass spectrometry
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Linda Z. Penn, Tharan Srikumar, Romina Ponzielli, Pak-Kei Chan, Sam S. Kim, David P. Bazett-Jones, Manpreet Kalkat, Amanda R. Wasylishen, and Brian Raught
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Cancer Research ,biology ,Oncogene ,Immunoprecipitation ,SUMO protein ,Ubiquitin ligase ,Oncology ,Ubiquitin ,biology.protein ,Transcriptional regulation ,Cancer research ,Phosphorylation ,Molecular Biology ,Transcription factor - 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.
- Published
- 2015
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29. Abstract A10: The myc post-translational landscape: How novel gain-of-function mutants are revealing new stability and functional regulatory systems
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Pak-Kei Chan, Dharmendra Dingar, Brian Raught, Peter J. Mullen, Corey Lourenco, Michelle Chan-Seng-Yue, William B. Tu, Manpreet Kalkat, Christina Bros, Amanda R. Wasylishen, Linda Z. Penn, and Paul C. Boutros
- Subjects
Cancer Research ,Oncogene ,Mutant ,SUMO protein ,Biology ,Molecular biology ,Deubiquitinating enzyme ,Oncology ,Ubiquitin ,Acetylation ,biology.protein ,Phosphorylation ,Signal transduction ,Molecular Biology - 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.
- Published
- 2015
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30. Abstract B04: In vivo BioID identifies novel Myc interacting partners
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Tharan Srikumar, Swneke D. Bailey, Etienne Coyaud, Annie Huang, Max Kolyar, Pak-Kei Chan, Dharmendra Dingar, William B. Tu, Igor Jurisica, Linda Z. Penn, Mathieu Lupien, Manpreet Kalkat, Romina Ponzielli, and Brian Raught
- Subjects
Lysine Acetyltransferase 5 ,Cancer Research ,Two-hybrid screening ,Biology ,medicine.disease_cause ,Interactome ,Chromodomain ,Oncology ,Transcription (biology) ,Cancer research ,medicine ,KAT5 ,Enhancer ,Carcinogenesis ,Molecular Biology - 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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- 2015
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31. Abstract A36: Interaction of the MYC oncoprotein with the tumor suppressive SWI/SNF complex member INI1
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Pak-Kei Chan, Brian Raught, Paul C. Boutros, Max Kotlyar, Linda Z. Penn, Igor Jurisica, William B. Tu, Fereshteh Khosravi, Romina Ponzielli, and Angelina Stojanova
- Subjects
Cancer Research ,Leucine zipper ,Oncology ,SWI/SNF complex ,Oncogene ,Cancer research ,Context (language use) ,Epigenetics ,SMARCB1 ,Biology ,Molecular Biology ,Chromatin remodeling ,Chromatin - 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.
- Published
- 2015
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32. A Strategy for Modulation of Enzymes in the Ubiquitin System.
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Ernst, Andreas, Awakumov, George, Jiefei Tong, Yihui Fan, Yanling Zhao, Alberts, Philipp, Persaud, Avinash, Walker, John R., Neculai, Ana-Mirela, Neculai, Dante, Vorobyov, Andrew, Garg, Pankaj, Beatty, Linda, Pak-Kei Chan, Yu-Chi Juang, Landry, Marie-Claude, Yeh, Christina, Zeqiraj, Elton, Karamboulas, Konstantina, and Atlali-Hassani, Abdellah
- Subjects
- *
UBIQUITINATION , *UBIQUITIN , *ENZYME inhibitors synthesis , *UBIQUITIN ligases , *UBIQUITIN-conjugating enzymes , *PROTEOLYTIC enzyme regulation , *BINDING sites , *ENZYME specificity , *DNA probes , *PHARMACEUTICAL research - Abstract
The article describes the analysis of the enzymes implicated in the protein ubiquitination system in cells, with particular focus on deubiquitinating enzymes, or deubiquitinases (DUBs). Enzyme inhibitors were designed for DUBs such as ubiquitin-specific proteases (USPs), as well as ubiquitin-conjugating enzymes and ubiquitin ligases. Crystallography of the enzyme-inhibitors complexes indicated that enzyme activity was modulated by the use of different ubiquitin variants. The researchers also investigated ubiquitin-binding domain selectivity of various ubiquitin variants. It is suggested that the regulation of enzyme activity by ubiquitin variants would make them an effective genetic probe in drug discovery research.
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- 2013
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33. Mannich Reactions in Room Temperature Ionic Liquids (RTILs): An Advanced Undergraduate Project of Green Chemistry and Structural Elucidation.
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Mak, Kendrew K. W., Siu, Jane, Lai, Y. M., and Pak-Kei Chan
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- *
MANNICH reaction , *CHEMICAL reactions , *CHEMISTRY education , *ACTIVITY programs in education , *CHEMICAL processes , *CHEMICAL reactors , *IONIC solutions , *RESEARCH , *SCIENCE education - Abstract
The article discusses a study on the mannich reactions in room temperature ionic liquids (RTIL). The project which took 4 laboratory sessions to complete, involves several experimental works which includes the preparation of the RTIL 1-butyl-3-methyl-imidazolium tetrafluoroborate, [bmim][BF4]; the investigation of the effectiveness of [bmim][BF4] as a recyclable reaction medium for the Mannich reactions; and the spectroscopic characterization of the products of the reaction. This project offers students a great opportunity to work on a current research area and to experience research oriented work related to postgraduate studies.
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- 2006
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34. Proteomic Profiling of the Human Cytomegalovirus UL35 Gene Products Reveals a Role for UL35 in the DNA Repair Response.
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Salsman, Jayme, Jagannathan, Madhav, Paladino, Patrick, Pak-Kei Chan, Dellaire, Graham, Raught, Brian, and Frappier, Lori
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- *
PROTEOMICS , *HUMAN cytomegalovirus - Abstract
An abstract of the article "Proteomic Profiling of the Human Cytomegalovirus UL35 Gene Products Reveals a Role for UL35 in the DNA Repair Response," by Jayme Salsman and colleagues is presented.
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- 2012
- Full Text
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