1
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Hartley B, Bassiouni W, Roczkowsky A, Fahlman R, Schulz R, Julien O. N-Terminomic Identification of Intracellular MMP-2 Substrates in Cardiac Tissue. J Proteome Res 2024. [PMID: 38647137 DOI: 10.1021/acs.jproteome.3c00755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Proteases are enzymes that induce irreversible post-translational modifications by hydrolyzing amide bonds in proteins. One of these proteases is matrix metalloproteinase-2 (MMP-2), which has been shown to modulate extracellular matrix remodeling and intracellular proteolysis during myocardial injury. However, the substrates of MMP-2 in heart tissue are limited, and lesser known are the cleavage sites. Here, we used degradomics to investigate the substrates of intracellular MMP-2 in rat ventricular extracts. First, we designed a novel, constitutively active MMP-2 fusion protein (MMP-2-Fc) that we expressed and purified from mammalian cells. Using this protease, we proteolyzed ventricular extracts and used subtiligase-mediated N-terminomic labeling which identified 95 putative MMP-2-Fc proteolytic cleavage sites using mass spectrometry. The intracellular MMP-2 cleavage sites identified in heart tissue extracts were enriched for proteins primarily involved in metabolism, as well as the breakdown of fatty acids and amino acids. We further characterized the cleavage of three of these MMP-2-Fc substrates based on the gene ontology analysis. We first characterized the cleavage of sarco/endoplasmic reticulum calcium ATPase (SERCA2a), a known MMP-2 substrate in myocardial injury. We then characterized the cleavage of malate dehydrogenase (MDHM) and phosphoglycerate kinase 1 (PGK1), representing new cardiac tissue substrates. Our findings provide insights into the intracellular substrates of MMP-2 in cardiac cells, suggesting that MMP-2 activation plays a role in cardiac metabolism.
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Affiliation(s)
- Bridgette Hartley
- Department of Biochemistry, University of Alberta, Edmonton T6G 2H7, Canada
| | - Wesam Bassiouni
- Department of Pharmacology, University of Alberta, Edmonton T6G 2S2, Canada
| | - Andrej Roczkowsky
- Department of Pharmacology, University of Alberta, Edmonton T6G 2S2, Canada
| | - Richard Fahlman
- Department of Biochemistry, University of Alberta, Edmonton T6G 2H7, Canada
| | - Richard Schulz
- Department of Pharmacology, University of Alberta, Edmonton T6G 2S2, Canada
- Department of Pediatrics, University of Alberta, Edmonton T6G 2S2, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton T6G 2H7, Canada
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2
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Ibtisam I, Kisselev AF. Early recovery of proteasome activity in cells pulse-treated with proteasome inhibitors is independent of DDI2. eLife 2024; 12:RP91678. [PMID: 38619391 PMCID: PMC11018354 DOI: 10.7554/elife.91678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Abstract
Rapid recovery of proteasome activity may contribute to intrinsic and acquired resistance to FDA-approved proteasome inhibitors. Previous studies have demonstrated that the expression of proteasome genes in cells treated with sub-lethal concentrations of proteasome inhibitors is upregulated by the transcription factor Nrf1 (NFE2L1), which is activated by a DDI2 protease. Here, we demonstrate that the recovery of proteasome activity is DDI2-independent and occurs before transcription of proteasomal genes is upregulated but requires protein translation. Thus, mammalian cells possess an additional DDI2 and transcription-independent pathway for the rapid recovery of proteasome activity after proteasome inhibition.
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Affiliation(s)
- Ibtisam Ibtisam
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn UniversityAuburnUnited States
| | - Alexei F Kisselev
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn UniversityAuburnUnited States
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3
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Ibtisam I, Kisselev AF. Early recovery of proteasome activity in cells pulse-treated with proteasome inhibitors is independent of DDI2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.550647. [PMID: 37577495 PMCID: PMC10418215 DOI: 10.1101/2023.08.03.550647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Rapid recovery of proteasome activity may contribute to intrinsic and acquired resistance to FDA-approved proteasome inhibitors. Previous studies have demonstrated that the expression of proteasome genes in cells treated with sub-lethal concentrations of proteasome inhibitors is upregulated by the transcription factor Nrf1 (NFE2L1), which is activated by a DDI2 protease. Here, we demonstrate that the recovery of proteasome activity is DDI2-independent and occurs before transcription of proteasomal genes is upregulated but requires protein translation. Thus, mammalian cells possess an additional DDI2 and transcription-independent pathway for the rapid recovery of proteasome activity after proteasome inhibition.
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Affiliation(s)
- Ibtisam Ibtisam
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn University, 720 S. Donahue Dr. Auburn AL 36849 USA
| | - Alexei F. Kisselev
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn University, 720 S. Donahue Dr. Auburn AL 36849 USA
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4
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Martin B, Suter DM. Gene expression flux analysis reveals specific regulatory modalities of gene expression. iScience 2023; 26:107758. [PMID: 37701574 PMCID: PMC10493597 DOI: 10.1016/j.isci.2023.107758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/02/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
The level of a given protein is determined by the synthesis and degradation rates of its mRNA and protein. While several studies have quantified the contribution of different gene expression steps in regulating protein levels, these are limited by using equilibrium approximations in out-of-equilibrium biological systems. Here, we introduce gene expression flux analysis to quantitatively dissect the dynamics of the expression level for specific proteins and use it to analyze published transcriptomics and proteomics datasets. Our analysis reveals distinct regulatory modalities shared by sets of genes with clear functional signatures. We also find that protein degradation plays a stronger role than expected in the adaptation of protein levels. These findings suggest that shared regulatory strategies can lead to versatile responses at the protein level and highlight the importance of going beyond equilibrium approximations to dissect the quantitative contribution of different steps of gene expression to protein dynamics.
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Affiliation(s)
- Benjamin Martin
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - David M. Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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5
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Zhai LH, Chen KF, Hao BB, Tan MJ. Proteomic characterization of post-translational modifications in drug discovery. Acta Pharmacol Sin 2022; 43:3112-3129. [PMID: 36372853 PMCID: PMC9712763 DOI: 10.1038/s41401-022-01017-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/07/2022] [Indexed: 11/15/2022] Open
Abstract
Protein post-translational modifications (PTMs), which are usually enzymatically catalyzed, are major regulators of protein activity and involved in almost all celluar processes. Dysregulation of PTMs is associated with various types of diseases. Therefore, PTM regulatory enzymes represent as an attractive and important class of targets in drug research and development. Inhibitors against kinases, methyltransferases, deacetyltransferases, ubiquitin ligases have achieved remarkable success in clinical application. Mass spectrometry-based proteomics technologies serve as a powerful approach for system-wide characterization of PTMs, which facilitates the identification of drug targets, elucidation of the mechanisms of action of drugs, and discovery of biomakers in personalized therapy. In this review, we summarize recent advances of proteomics-based studies on PTM targeting drugs and discuss how proteomics strategies facilicate drug target identification, mechanism elucidation, and new therapy development in precision medicine.
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Affiliation(s)
- Lin-Hui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China
| | - Kai-Feng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing-Bing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Min-Jia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China.
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6
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Watson J, Ferguson HR, Brady RM, Ferguson J, Fullwood P, Mo H, Bexley KH, Knight D, Howell G, Schwartz JM, Smith MP, Francavilla C. Spatially resolved phosphoproteomics reveals fibroblast growth factor receptor recycling-driven regulation of autophagy and survival. Nat Commun 2022; 13:6589. [PMID: 36329028 DOI: 10.1101/2021.01.17.427038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 10/19/2022] [Indexed: 05/26/2023] Open
Abstract
Receptor Tyrosine Kinase (RTK) endocytosis-dependent signalling drives cell proliferation and motility during development and adult homeostasis, but is dysregulated in diseases, including cancer. The recruitment of RTK signalling partners during endocytosis, specifically during recycling to the plasma membrane, is still unknown. Focusing on Fibroblast Growth Factor Receptor 2b (FGFR2b) recycling, we reveal FGFR signalling partners proximal to recycling endosomes by developing a Spatially Resolved Phosphoproteomics (SRP) approach based on APEX2-driven biotinylation followed by phosphorylated peptides enrichment. Combining this with traditional phosphoproteomics, bioinformatics, and targeted assays, we uncover that FGFR2b stimulated by its recycling ligand FGF10 activates mTOR-dependent signalling and ULK1 at the recycling endosomes, leading to autophagy suppression and cell survival. This adds to the growing importance of RTK recycling in orchestrating cell fate and suggests a therapeutically targetable vulnerability in ligand-responsive cancer cells. Integrating SRP with other systems biology approaches provides a powerful tool to spatially resolve cellular signalling.
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Affiliation(s)
- Joanne Watson
- Division of Evolution, Infection and Genomics, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Harriet R Ferguson
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Rosie M Brady
- Division of Cancer Sciences, School of Medical Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, Manchester, M20 4GJ, UK
| | - Jennifer Ferguson
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Paul Fullwood
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Hanyi Mo
- Division of Evolution, Infection and Genomics, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Katherine H Bexley
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - David Knight
- Bio-MS Core Research Facility, FBMH, The University of Manchester, M139PT, Manchester, UK
| | - Gareth Howell
- Flow Cytometry Core Research Facility, FBMH, The University of Manchester, M139PT, Manchester, UK
| | - Jean-Marc Schwartz
- Division of Evolution, Infection and Genomics, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Michael P Smith
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK.
| | - Chiara Francavilla
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK.
- Manchester Breast Centre, Manchester Cancer Research Centre, The University of Manchester, M139PT, Manchester, UK.
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7
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Ferguson ID, Lin YHT, Lam C, Shao H, Tharp KM, Hale M, Kasap C, Mariano MC, Kishishita A, Patiño Escobar B, Mandal K, Steri V, Wang D, Phojanakong P, Tuomivaara ST, Hann B, Driessen C, Van Ness B, Gestwicki JE, Wiita AP. Allosteric HSP70 inhibitors perturb mitochondrial proteostasis and overcome proteasome inhibitor resistance in multiple myeloma. Cell Chem Biol 2022; 29:1288-1302.e7. [PMID: 35853457 PMCID: PMC9434701 DOI: 10.1016/j.chembiol.2022.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/21/2022] [Accepted: 06/24/2022] [Indexed: 11/03/2022]
Abstract
Proteasome inhibitor (PI) resistance remains a central challenge in multiple myeloma. To identify pathways mediating resistance, we first mapped proteasome-associated genetic co-dependencies. We identified heat shock protein 70 (HSP70) chaperones as potential targets, consistent with proposed mechanisms of myeloma cells overcoming PI-induced stress. We therefore explored allosteric HSP70 inhibitors (JG compounds) as myeloma therapeutics. JG compounds exhibited increased efficacy against acquired and intrinsic PI-resistant myeloma models, unlike HSP90 inhibition. Shotgun and pulsed SILAC mass spectrometry demonstrated that JGs unexpectedly impact myeloma proteostasis by destabilizing the 55S mitoribosome. Our data suggest JGs have the most pronounced anti-myeloma effect not through inhibiting cytosolic HSP70 proteins but instead through mitochondrial-localized HSP70, HSPA9/mortalin. Analysis of myeloma patient data further supports strong effects of global proteostasis capacity, and particularly HSPA9 expression, on PI response. Our results characterize myeloma proteostasis networks under therapeutic pressure while motivating further investigation of HSPA9 as a specific vulnerability in PI-resistant disease.
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Affiliation(s)
- Ian D Ferguson
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Yu-Hsiu T Lin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Christine Lam
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Hao Shao
- Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevin M Tharp
- Department of Surgery, University of California, San Francisco, San Francisco CA 94143, USA
| | - Martina Hale
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Corynn Kasap
- Department of Medicine, Division of Hematology or Oncology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Margarette C Mariano
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Audrey Kishishita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA; Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bonell Patiño Escobar
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Kamal Mandal
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Donghui Wang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Paul Phojanakong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sami T Tuomivaara
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Byron Hann
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christoph Driessen
- Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Brian Van Ness
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jason E Gestwicki
- Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA.
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8
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Ferguson ID, Patiño-Escobar B, Tuomivaara ST, Lin YHT, Nix MA, Leung KK, Kasap C, Ramos E, Nieves Vasquez W, Talbot A, Hale M, Naik A, Kishishita A, Choudhry P, Lopez-Girona A, Miao W, Wong SW, Wolf JL, Martin TG, Shah N, Vandenberg S, Prakash S, Besse L, Driessen C, Posey AD, Mullins RD, Eyquem J, Wells JA, Wiita AP. The surfaceome of multiple myeloma cells suggests potential immunotherapeutic strategies and protein markers of drug resistance. Nat Commun 2022; 13:4121. [PMID: 35840578 PMCID: PMC9287322 DOI: 10.1038/s41467-022-31810-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/30/2022] [Indexed: 12/21/2022] Open
Abstract
The myeloma surface proteome (surfaceome) determines tumor interaction with the microenvironment and serves as an emerging arena for therapeutic development. Here, we use glycoprotein capture proteomics to define the myeloma surfaceome at baseline, in drug resistance, and in response to acute drug treatment. We provide a scoring system for surface antigens and identify CCR10 as a promising target in this disease expressed widely on malignant plasma cells. We engineer proof-of-principle chimeric antigen receptor (CAR) T-cells targeting CCR10 using its natural ligand CCL27. In myeloma models we identify proteins that could serve as markers of resistance to bortezomib and lenalidomide, including CD53, CD10, EVI2B, and CD33. We find that acute lenalidomide treatment increases activity of MUC1-targeting CAR-T cells through antigen upregulation. Finally, we develop a miniaturized surface proteomic protocol for profiling primary plasma cell samples with low inputs. These approaches and datasets may contribute to the biological, therapeutic, and diagnostic understanding of myeloma.
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Affiliation(s)
- Ian D Ferguson
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sami T Tuomivaara
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Yu-Hsiu T Lin
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Matthew A Nix
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Corynn Kasap
- Department of Medicine, Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - Emilio Ramos
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Wilson Nieves Vasquez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Alexis Talbot
- Department of Medicine, Division of Hematology/Oncology, University of California, San Francisco, CA, USA
- INSERM U976, Institut de Recherche Saint Louis, Université de Paris, Paris, France
| | - Martina Hale
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Akul Naik
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Audrey Kishishita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Program in Chemistry and Chemical Biology, University of California, San Francisco, CA, USA
| | - Priya Choudhry
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | - Weili Miao
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sandy W Wong
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Jeffrey L Wolf
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Thomas G Martin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Nina Shah
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Scott Vandenberg
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Sonam Prakash
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Lenka Besse
- Department of Medical Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Christoph Driessen
- Department of Medical Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Avery D Posey
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - R Dyche Mullins
- Department of Medicine, Division of Hematology/Oncology, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Justin Eyquem
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Gladstone Institute for Genomic Immunology, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
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9
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Effects of Cancer Presence and Therapy on the Platelet Proteome. Int J Mol Sci 2021; 22:ijms22158236. [PMID: 34361002 PMCID: PMC8347210 DOI: 10.3390/ijms22158236] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/27/2022] Open
Abstract
Platelets are involved in tumor angiogenesis and cancer progression. Previous studies indicated that cancer could affect platelet content. In the current study, we investigated whether cancer-associated proteins can be discerned in the platelets of cancer patients, and whether antitumor treatment may affect the platelet proteome. Platelets were isolated from nine patients with different cancer types and ten healthy volunteers. From three patients, platelets were isolated before and after the start of antitumor treatment. Mass spectrometry-based proteomics of gel-fractionated platelet proteins were used to compare patients versus controls and before and after treatment initiation. A total of 4059 proteins were detected, of which 50 were significantly more abundant in patients, and 36 more in healthy volunteers. Eight of these proteins overlapped with our previous cancer platelet proteomics study. From these data, we selected potential biomarkers of cancer including six upregulated proteins (RNF213, CTSG, PGLYRP1, RPL8, S100A8, S100A9) and two downregulated proteins (GPX1, TNS1). Antitumor treatment resulted in increased levels of 432 proteins and decreased levels of 189 proteins. In conclusion, the platelet proteome may be affected in cancer patients and platelets are a potential source of cancer biomarkers. In addition, we found in a small group of patients that anticancer treatment significantly changes the platelet proteome.
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10
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Huang HH, Ferguson ID, Thornton AM, Bastola P, Lam C, Lin YHT, Choudhry P, Mariano MC, Marcoulis MD, Teo CF, Malato J, Phojanakong PJ, Martin TG, Wolf JL, Wong SW, Shah N, Hann B, Brooks AN, Wiita AP. Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma. Nat Commun 2020; 11:1931. [PMID: 32321912 PMCID: PMC7176739 DOI: 10.1038/s41467-020-15521-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/13/2020] [Indexed: 02/06/2023] Open
Abstract
Enhancing the efficacy of proteasome inhibitors (PI) is a central goal in myeloma therapy. We proposed that signaling-level responses after PI may reveal new mechanisms of action that can be therapeutically exploited. Unbiased phosphoproteomics after treatment with the PI carfilzomib surprisingly demonstrates the most prominent phosphorylation changes on splicing related proteins. Spliceosome modulation is invisible to RNA or protein abundance alone. Transcriptome analysis after PI demonstrates broad-scale intron retention, suggestive of spliceosome interference, as well as specific alternative splicing of protein homeostasis machinery components. These findings lead us to evaluate direct spliceosome inhibition in myeloma, which synergizes with carfilzomib and shows potent anti-tumor activity. Functional genomics and exome sequencing further support the spliceosome as a specific vulnerability in myeloma. Our results propose splicing interference as an unrecognized modality of PI mechanism, reveal additional modes of spliceosome modulation, and suggest spliceosome targeting as a promising therapeutic strategy in myeloma.
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Affiliation(s)
- Hector H Huang
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Ian D Ferguson
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Alexis M Thornton
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Prabhakar Bastola
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Christine Lam
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Yu-Hsiu T Lin
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Priya Choudhry
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Margarette C Mariano
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Makeba D Marcoulis
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Chin Fen Teo
- Department of Physiology, University of California, San Francisco, CA, USA
| | - Julia Malato
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Paul J Phojanakong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Thomas G Martin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Jeffrey L Wolf
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Sandy W Wong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Nina Shah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Byron Hann
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
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11
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Smekalova EM, Gerashchenko MV, O'Connor PBF, Whittaker CA, Kauffman KJ, Fefilova AS, Zatsepin TS, Bogorad RL, Baranov PV, Langer R, Gladyshev VN, Anderson DG, Koteliansky V. In Vivo RNAi-Mediated eIF3m Knockdown Affects Ribosome Biogenesis and Transcription but Has Limited Impact on mRNA-Specific Translation. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:252-266. [PMID: 31855834 PMCID: PMC6926209 DOI: 10.1016/j.omtn.2019.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/20/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022]
Abstract
Translation is an essential biological process, and dysregulation is associated with a range of diseases including ribosomopathies, diabetes, and cancer. Here, we examine translation dysregulation in vivo using RNAi to knock down the m-subunit of the translation initiation factor eIF3 in the mouse liver. Transcriptome sequencing, ribosome profiling, whole proteome, and phosphoproteome analyses show that eIF3m deficiency leads to the transcriptional response and changes in cellular translation that yield few detectable differences in the translation of particular mRNAs. The transcriptional response fell into two main categories: ribosome biogenesis (increased transcription of ribosomal proteins) and cell metabolism (alterations in lipid, amino acid, nucleic acid, and drug metabolism). Analysis of ribosome biogenesis reveals inhibition of rRNA processing, highlighting decoupling of rRNA synthesis and ribosomal protein gene transcription in response to eIF3m knockdown. Interestingly, a similar reduction in eIF3m protein levels is associated with induction of the mTOR pathway in vitro but not in vivo. Overall, this work highlights the utility of a RNAi-based in vivo approach for studying the regulation of mammalian translation in vivo.
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Affiliation(s)
- Elena M Smekalova
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Patrick B F O'Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Charles A Whittaker
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kevin J Kauffman
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Anna S Fefilova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia; Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia.
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12
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Lessons Learned from Proteasome Inhibitors, the Paradigm for Targeting Protein Homeostasis in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1243:147-162. [PMID: 32297217 DOI: 10.1007/978-3-030-40204-4_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Targeting aberrant protein homeostasis (proteostasis) in cancer is an attractive therapeutic strategy. However, this approach has thus far proven difficult to bring to clinical practice, with one major exception: proteasome inhibition. These small molecules have dramatically transformed outcomes for patients with the blood cancer multiple myeloma. However, these agents have failed to make an impact in more common solid tumors. Major questions remain about whether this therapeutic strategy can be extended to benefit even more patients. Here we discuss the role of the proteasome in normal and tumor cells, the basic, preclinical, and clinical development of proteasome inhibitors, and mechanisms proposed to govern both intrinsic and acquired resistance to these drugs. Years of study of both the mechanism of action and modes of resistance to proteasome inhibitors reveal these processes to be surprisingly complex. Here, we attempt to draw lessons from experience with proteasome inhibitors that may be relevant for other compounds targeting proteostasis in cancer, as well as extending the reach of proteasome inhibitors beyond blood cancers.
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13
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Abstract
Proteases are key regulators of vital biological processes, such as apoptosis, cell differentiation, viral infection and neurodegeneration. Proteases are tightly regulated, largely because proteolysis is a unique post-translational modification (PTM) that is essentially irreversible. In order to understand the role of proteases in health and disease, the identification of protease substrates is an important step toward our understanding of their biological functions. Classic approaches for the study of proteolysis in complex mixtures employ gel electrophoresis and mass spectrometry. Such approaches typically identify a few protein substrates at a time but often fail to identify specific cleavage site locations. In contrast, modern proteomic methods using enrichment of proteolytic protein fragments can lead to the identification of hundreds of modified peptides with precise cleavage site determination in a single experiment. In this manuscript, we will review recent advances in N-terminomics methods and highlight key studies that have taken advantage of these technologies to advance our understanding of the role of proteases in cellular physiology.
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Affiliation(s)
- Shu Yue Luo
- Department of Biochemistry, University of Alberta, Edmonton, Alberta Canada
| | - Luam Ellen Araya
- Department of Biochemistry, University of Alberta, Edmonton, Alberta Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, Alberta Canada
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14
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Weng SSH, Demir F, Ergin EK, Dirnberger S, Uzozie A, Tuscher D, Nierves L, Tsui J, Huesgen PF, Lange PF. Sensitive Determination of Proteolytic Proteoforms in Limited Microscale Proteome Samples. Mol Cell Proteomics 2019; 18:2335-2347. [PMID: 31471496 PMCID: PMC6823850 DOI: 10.1074/mcp.tir119.001560] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/09/2019] [Indexed: 12/15/2022] Open
Abstract
Protein N termini unambiguously identify truncated, alternatively translated or modified proteoforms with distinct functions and reveal perturbations in disease. Selective enrichment of N-terminal peptides is necessary to achieve proteome-wide coverage for unbiased identification of site-specific regulatory proteolytic processing and protease substrates. However, many proteolytic processes are strictly confined in time and space and therefore can only be analyzed in minute samples that provide insufficient starting material for current enrichment protocols. Here we present High-efficiency Undecanal-based N Termini EnRichment (HUNTER), a robust, sensitive and scalable method for the analysis of previously inaccessible microscale samples. HUNTER achieved identification of >1000 N termini from as little as 2 μg raw HeLa cell lysate. Broad applicability is demonstrated by the first N-terminome analysis of sorted human primary immune cells and enriched mitochondrial fractions from pediatric cancer patients, as well as protease substrate identification from individual Arabidopsis thaliana wild type and Vacuolar Processing Enzyme-deficient mutant seedlings. We further implemented the workflow on a liquid handling system and demonstrate the feasibility of clinical degradomics by automated processing of liquid biopsies from pediatric cancer patients.
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Affiliation(s)
- Samuel S H Weng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Enes K Ergin
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Sabrina Dirnberger
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Anuli Uzozie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Domenic Tuscher
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Lorenz Nierves
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Janice Tsui
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
| | - Philipp F Lange
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada.
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15
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Abstract
Subtiligase-catalyzed peptide ligation is a powerful approach for site-specific protein bioconjugation, synthesis and semisynthesis of proteins and peptides, and chemoproteomic analysis of cellular N termini. Here, we provide a comprehensive review of the subtiligase technology, including its development, applications, and impacts on protein science. We highlight key advantages and limitations of the tool and compare it to other peptide ligase enzymes. Finally, we provide a perspective on future applications and challenges and how they may be addressed.
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Affiliation(s)
- Amy M Weeks
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94143, United States
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16
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Xu Z, Hu L, Shi B, Geng S, Xu L, Wang D, Lu ZJ. Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events. Nucleic Acids Res 2019; 46:e109. [PMID: 29945224 PMCID: PMC6182183 DOI: 10.1093/nar/gky533] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/31/2018] [Indexed: 02/06/2023] Open
Abstract
Translation is dynamically regulated during cell development and stress response. In order to detect actively translated open reading frames (ORFs) and dynamic cellular translation events, we have developed a computational method, RiboWave, to process ribosome profiling data. RiboWave utilizes wavelet transform to denoise the original signal by extracting 3-nt periodicity of ribosomes and precisely locate their footprint denoted as Periodic Footprint P-site (PF P-site). Such high-resolution footprint is found to capture the full track of actively elongating ribosomes, from which translational landscape can be explicitly characterized. We compare RiboWave with several published methods, like RiboTaper, ORFscore and RibORF, and found that RiboWave outperforms them in both accuracy and usage when defining actively translated ORFs. Moreover, we show that PF P-site derived by RiboWave shows superior performance in characterizing the dynamics and complexity of cellular translatome by accurately estimating the abundance of protein levels, assessing differential translation and identifying dynamic translation frameshift.
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Affiliation(s)
- Zhiyu Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Long Hu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Binbin Shi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - SiSi Geng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Longchen Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dong Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhi J Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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17
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Michel AM, Kiniry SJ, O'Connor PBF, Mullan JP, Baranov PV. GWIPS-viz: 2018 update. Nucleic Acids Res 2019; 46:D823-D830. [PMID: 28977460 PMCID: PMC5753223 DOI: 10.1093/nar/gkx790] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 08/29/2017] [Indexed: 12/15/2022] Open
Abstract
The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been automated thereby increasing the number of available tracks to 1792, a 10-fold increase in the last three years. The increase is particularly substantial for data derived from human sources. Following user requests, we added the functionality to download these tracks in bigWig format. We also incorporated new types of data (e.g. TCP-seq) as well as auxiliary tracks from other sources that help with the interpretation of Ribo-seq data. Improvements in the visualization of the data have been carried out particularly for bacterial genomes where the Ribo-seq data are now shown in a strand specific manner. For higher eukaryotic datasets, we provide characteristics of individual datasets using the RUST program which includes the triplet periodicity, sequencing biases and relative inferred A-site dwell times. This information can be used for assessing the quality of Ribo-seq datasets. To improve the power of the signal, we aggregate Ribo-seq data from several studies into Global aggregate tracks for each genome.
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Affiliation(s)
- Audrey M Michel
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | | | - James P Mullan
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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18
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McGillivray P, Ault R, Pawashe M, Kitchen R, Balasubramanian S, Gerstein M. A comprehensive catalog of predicted functional upstream open reading frames in humans. Nucleic Acids Res 2019; 46:3326-3338. [PMID: 29562350 PMCID: PMC6283423 DOI: 10.1093/nar/gky188] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/14/2018] [Indexed: 01/09/2023] Open
Abstract
Upstream open reading frames (uORFs) latent in mRNA transcripts are thought to modify translation of coding sequences by altering ribosome activity. Not all uORFs are thought to be active in such a process. To estimate the impact of uORFs on the regulation of translation in humans, we first circumscribed the universe of all possible uORFs based on coding gene sequence motifs and identified 1.3 million unique uORFs. To determine which of these are likely to be biologically relevant, we built a simple Bayesian classifier using 89 attributes of uORFs labeled as active in ribosome profiling experiments. This allowed us to extrapolate to a comprehensive catalog of likely functional uORFs. We validated our predictions using in vivo protein levels and ribosome occupancy from 46 individuals. This is a substantially larger catalog of functional uORFs than has previously been reported. Our ranked list of likely active uORFs allows researchers to test their hypotheses regarding the role of uORFs in health and disease. We demonstrate several examples of biological interest through the application of our catalog to somatic mutations in cancer and disease-associated germline variants in humans.
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Affiliation(s)
- Patrick McGillivray
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
| | - Russell Ault
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
| | - Mayur Pawashe
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
| | - Robert Kitchen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Suganthi Balasubramanian
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Mark Gerstein
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.,Department of Computer Science, Yale University, New Haven, CT 06520 USA
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19
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Multiomics of azacitidine-treated AML cells reveals variable and convergent targets that remodel the cell-surface proteome. Proc Natl Acad Sci U S A 2018; 116:695-700. [PMID: 30584089 DOI: 10.1073/pnas.1813666116] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are diseases of abnormal hematopoietic differentiation with aberrant epigenetic alterations. Azacitidine (AZA) is a DNA methyltransferase inhibitor widely used to treat MDS and AML, yet the impact of AZA on the cell-surface proteome has not been defined. To identify potential therapeutic targets for use in combination with AZA in AML patients, we investigated the effects of AZA treatment on four AML cell lines representing different stages of differentiation. The effect of AZA treatment on these cell lines was characterized at three levels: the DNA methylome, the transcriptome, and the cell-surface proteome. Untreated AML cell lines showed substantial overlap at all three omics levels; however, while AZA treatment globally reduced DNA methylation in all cell lines, changes in the transcriptome and surface proteome were subtle and differed among the cell lines. Transcriptome analysis identified five commonly up-regulated coding genes upon AZA treatment in all four cell lines, TRPM4 being the only gene encoding a surface protein, and surface proteome analysis found no commonly regulated proteins. Gene set enrichment analysis of differentially regulated RNA and surface proteins showed a decrease in metabolic pathways and an increase in immune defense response pathways. As such, AZA treatment led to diverse effects at the individual gene and protein levels but converged to common responses at the pathway level. Given the heterogeneous responses in the four cell lines, we discuss potential therapeutic strategies for AML in combination with AZA.
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20
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Patatsos K, Shekhar TM, Hawkins CJ. Pre-clinical evaluation of proteasome inhibitors for canine and human osteosarcoma. Vet Comp Oncol 2018; 16:544-553. [PMID: 29998615 DOI: 10.1111/vco.12413] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 04/30/2018] [Accepted: 05/29/2018] [Indexed: 12/12/2022]
Abstract
Osteosarcoma, a common malignancy in large dog breeds, typically metastasises from long bones to lungs and is usually fatal within 1 to 2 years of diagnosis. Better therapies are needed for canine patients and their human counterparts, a third of whom die within 5 years of diagnosis. We compared the in vitro sensitivity of canine osteosarcoma cells derived from 4 tumours to the currently used chemotherapy drugs doxorubicin and carboplatin, and 4 new anti-cancer drugs. Agents targeting histone deacetylases or PARP were ineffective. Two of the 4 cell lines were somewhat sensitive to the BH3-mimetic navitoclax. The proteasome inhibitor bortezomib potently induced caspase-dependent apoptosis, at concentrations substantially lower than levels detected in the bones and lungs of treated rodents. Co-treatment with bortezomib and either doxorubicin or carboplatin was more toxic to canine osteosarcoma cells than each agent alone. Newer proteasome inhibitors carfilzomib, ixazomib, oprozomib and delanzomib manifested similar activities to bortezomib. Human osteosarcoma cells were as sensitive to bortezomib as the canine cells, but slightly less sensitive to the newer drugs. Human osteoblasts were less sensitive to proteasome inhibition than osteosarcoma cells, but physiologically relevant concentrations were toxic. Such toxicity, if replicated in vivo, may impair bone growth and strength in adolescent human osteosarcoma patients, but may be tolerated by canine patients, which are usually diagnosed later in life. Proteasome inhibitors such as bortezomib may be useful for treating canine osteosarcoma, and ultimately may improve outcomes for human patients if their osteoblasts survive exposure in vivo, or if osteoblast toxicity can be managed.
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Affiliation(s)
- K Patatsos
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - T M Shekhar
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - C J Hawkins
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
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21
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Choudhry P, Galligan D, Wiita AP. Seeking Convergence and Cure with New Myeloma Therapies. Trends Cancer 2018; 4:567-582. [PMID: 30064664 DOI: 10.1016/j.trecan.2018.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 02/06/2023]
Abstract
For over a decade, the mainstay of multiple myeloma therapy has been small molecules that directly attack malignant plasma cell biology. However, potent immunotherapies have recently emerged, transforming the myeloma therapeutic landscape. Here we first review new promising strategies to target plasma cells through protein homeostasis and epigenetic modulators. We then discuss emerging immunotherapy strategies that are leading to dramatic results in patients. Finally, we focus on recent preclinical data suggesting that enforcing cell-surface antigen expression through small molecules may enhance immunotherapy efficacy and avoid resistance. We argue that these emerging observations point the way toward potential convergence between drug classes. With recent rapid progress we may finally be on the verge of the 'C' word: a cure for myeloma.
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Affiliation(s)
- Priya Choudhry
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; These authors contributed equally
| | - Derek Galligan
- Department of Medicine, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; These authors contributed equally
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
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22
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Fok JHL, Hedayat S, Zhang L, Aronson LI, Mirabella F, Pawlyn C, Bright MD, Wardell CP, Keats JJ, De Billy E, Rye CS, Chessum NEA, Jones K, Morgan GJ, Eccles SA, Workman P, Davies FE. HSF1 Is Essential for Myeloma Cell Survival and A Promising Therapeutic Target. Clin Cancer Res 2018; 24:2395-2407. [PMID: 29391353 PMCID: PMC6420136 DOI: 10.1158/1078-0432.ccr-17-1594] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/23/2017] [Accepted: 12/29/2017] [Indexed: 01/09/2023]
Abstract
Purpose: Myeloma is a plasma cell malignancy characterized by the overproduction of immunoglobulin, and is therefore susceptible to therapies targeting protein homeostasis. We hypothesized that heat shock factor 1 (HSF1) was an attractive therapeutic target for myeloma due to its direct regulation of transcriptional programs implicated in both protein homeostasis and the oncogenic phenotype. Here, we interrogate HSF1 as a therapeutic target in myeloma using bioinformatic, genetic, and pharmacologic means.Experimental Design: To assess the clinical relevance of HSF1, we analyzed publicly available patient myeloma gene expression datasets. Validation of this novel target was conducted in in vitro experiments using shRNA or inhibitors of the HSF1 pathway in human myeloma cell lines and primary cells as well as in in vivo human myeloma xenograft models.Results: Expression of HSF1 and its target genes were associated with poorer myeloma patient survival. ShRNA-mediated knockdown or pharmacologic inhibition of the HSF1 pathway with a novel chemical probe, CCT251236, or with KRIBB11, led to caspase-mediated cell death that was associated with an increase in EIF2α phosphorylation, CHOP expression and a decrease in overall protein synthesis. Importantly, both CCT251236 and KRIBB11 induced cytotoxicity in human myeloma cell lines and patient-derived primary myeloma cells with a therapeutic window over normal cells. Pharmacologic inhibition induced tumor growth inhibition and was well-tolerated in a human myeloma xenograft murine model with evidence of pharmacodynamic biomarker modulation.Conclusions: Taken together, our studies demonstrate the dependence of myeloma cells on HSF1 for survival and support the clinical evaluation of pharmacologic inhibitors of the HSF1 pathway in myeloma. Clin Cancer Res; 24(10); 2395-407. ©2018 AACRSee related commentary by Parekh, p. 2237.
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Affiliation(s)
- Jacqueline H L Fok
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Somaieh Hedayat
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Lei Zhang
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Lauren I Aronson
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Fabio Mirabella
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, London, United Kingdom
| | - Charlotte Pawlyn
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Michael D Bright
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Christopher P Wardell
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, London, United Kingdom
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jonathan J Keats
- Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Emmanuel De Billy
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Carl S Rye
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Nicola E A Chessum
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Keith Jones
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Gareth J Morgan
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Suzanne A Eccles
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Faith E Davies
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom.
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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23
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Naß J, Efferth T. Insights into apoptotic proteins in chemotherapy: quantification techniques and informing therapy choice. Expert Rev Proteomics 2018; 15:413-429. [DOI: 10.1080/14789450.2018.1468755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Janine Naß
- Department of Pharmaceutical Biology, Institute of Biochemistry and Pharmacy, Johannes Gutenberg University, Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Biochemistry and Pharmacy, Johannes Gutenberg University, Mainz, Germany
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24
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Translational reprogramming of colorectal cancer cells induced by 5-fluorouracil through a miRNA-dependent mechanism. Oncotarget 2018; 8:46219-46233. [PMID: 28515355 PMCID: PMC5542262 DOI: 10.18632/oncotarget.17597] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/06/2017] [Indexed: 11/25/2022] Open
Abstract
5-Fluorouracil (5-FU) is a widely used chemotherapeutic drug in colorectal cancer. Previous studies showed that 5-FU modulates RNA metabolism and mRNA expression. In addition, it has been reported that 5-FU incorporates into the RNAs constituting the translational machinery and that 5-FU affects the amount of some mRNAs associated with ribosomes. However, the impact of 5-FU on translational regulation remains unclear. Using translatome profiling, we report that a clinically relevant dose of 5-FU induces a translational reprogramming in colorectal cancer cell lines. Comparison of mRNA distribution between polysomal and non-polysomal fractions in response to 5-FU treatment using microarray quantification identified 313 genes whose translation was selectively regulated. These regulations were mostly stimulatory (91%). Among these genes, we showed that 5-FU increases the mRNA translation of HIVEP2, which encodes a transcription factor whose translation in normal condition is known to be inhibited by mir-155. In response to 5-FU, the expression of mir-155 decreases thus stimulating the translation of HIVEP2 mRNA. Interestingly, the 5-FU-induced increase in specific mRNA translation was associated with reduction of global protein synthesis. Altogether, these findings indicate that 5-FU promotes a translational reprogramming leading to the increased translation of a subset of mRNAs that involves at least for some of them, miRNA-dependent mechanisms. This study supports a still poorly evaluated role of translational control in drug response.
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25
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Lam C, Ferguson ID, Mariano MC, Lin YHT, Murnane M, Liu H, Smith GA, Wong SW, Taunton J, Liu JO, Mitsiades CS, Hann BC, Aftab BT, Wiita AP. Repurposing tofacitinib as an anti-myeloma therapeutic to reverse growth-promoting effects of the bone marrow microenvironment. Haematologica 2018; 103:1218-1228. [PMID: 29622655 PMCID: PMC6029548 DOI: 10.3324/haematol.2017.174482] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 03/15/2018] [Indexed: 12/20/2022] Open
Abstract
The myeloma bone marrow microenvironment promotes proliferation of malignant plasma cells and resistance to therapy. Activation of JAK/STAT signaling is thought to be a central component of these microenvironment-induced phenotypes. In a prior drug repurposing screen, we identified tofacitinib, a pan-JAK inhibitor Food and Drug Administration (FDA) approved for rheumatoid arthritis, as an agent that may reverse the tumor-stimulating effects of bone marrow mesenchymal stromal cells. Herein, we validated in vitro, in stromal-responsive human myeloma cell lines, and in vivo, in orthotopic disseminated xenograft models of myeloma, that tofacitinib showed efficacy in myeloma models. Furthermore, tofacitinib strongly synergized with venetoclax in coculture with bone marrow stromal cells but not in monoculture. Surprisingly, we found that ruxolitinib, an FDA approved agent targeting JAK1 and JAK2, did not lead to the same anti-myeloma effects. Combination with a novel irreversible JAK3-selective inhibitor also did not enhance ruxolitinib effects. Transcriptome analysis and unbiased phosphoproteomics revealed that bone marrow stromal cells stimulate a JAK/STAT-mediated proliferative program in myeloma cells, and tofacitinib reversed the large majority of these pro-growth signals. Taken together, our results suggest that tofacitinib reverses the growth-promoting effects of the tumor microenvironment. As tofacitinib is already FDA approved, these results can be rapidly translated into potential clinical benefits for myeloma patients.
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Affiliation(s)
- Christine Lam
- Department of Laboratory Medicine, University of California, San Francisco, CA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Ian D Ferguson
- Department of Laboratory Medicine, University of California, San Francisco, CA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Margarette C Mariano
- Department of Laboratory Medicine, University of California, San Francisco, CA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Yu-Hsiu T Lin
- Department of Laboratory Medicine, University of California, San Francisco, CA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Megan Murnane
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA.,Department of Medicine, University of California, San Francisco, CA
| | - Hui Liu
- Department of Laboratory Medicine, University of California, San Francisco, CA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Geoffrey A Smith
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA
| | - Sandy W Wong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA.,Department of Medicine, University of California, San Francisco, CA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA
| | - Jun O Liu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | | | - Byron C Hann
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Blake T Aftab
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA.,Department of Medicine, University of California, San Francisco, CA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
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26
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Shah SP, Nooka AK, Jaye DL, Bahlis NJ, Lonial S, Boise LH. Bortezomib-induced heat shock response protects multiple myeloma cells and is activated by heat shock factor 1 serine 326 phosphorylation. Oncotarget 2018; 7:59727-59741. [PMID: 27487129 PMCID: PMC5312344 DOI: 10.18632/oncotarget.10847] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/18/2016] [Indexed: 12/22/2022] Open
Abstract
Proteasome inhibitors such as bortezomib are highly active in multiple myeloma by affecting signaling cascades and leading to a toxic buildup of misfolded proteins. Bortezomib-treated cells activate the cytoprotective heat shock response (HSR), including upregulation of heat shock proteins (HSPs). Here we inhibited the bortezomib-induced HSR by silencing its master regulator, Heat Shock Factor 1 (HSF1). HSF1 silencing led to bortezomib sensitization. In contrast, silencing of individual and combination HSPs, except HSP40β, did not result in significant bortezomib sensitization. However, HSP40β did not entirely account for increased bortezomib sensitivity upon HSF1 silencing. To determine the mechanism of HSF1 activation, we assessed phosphorylation and observed bortezomib-inducible phosphorylation in cell lines and patient samples. We determined that this bortezomib-inducible event is phosphorylation at serine 326. Prior clinical use of HSP inhibitors in combination with bortezomib has been disappointing in multiple myeloma therapy. Our results provide a rationale for targeting HSF1 activation in combination with bortezomib to enhance multiple myeloma treatment efficacy.
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Affiliation(s)
- Shardule P Shah
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University and the Emory University School of Medicine, Atlanta, GA, USA
| | - Ajay K Nooka
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University and the Emory University School of Medicine, Atlanta, GA, USA
| | - David L Jaye
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University and the Emory University School of Medicine, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Nizar J Bahlis
- Department of Medical Oncology and Hematology, Tom Baker Cancer Center, Calgary, AB, Canada
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University and the Emory University School of Medicine, Atlanta, GA, USA
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University and the Emory University School of Medicine, Atlanta, GA, USA
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27
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Laumont CM, Perreault C. Exploiting non-canonical translation to identify new targets for T cell-based cancer immunotherapy. Cell Mol Life Sci 2018; 75:607-621. [PMID: 28823056 PMCID: PMC11105255 DOI: 10.1007/s00018-017-2628-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/03/2017] [Accepted: 08/16/2017] [Indexed: 01/11/2023]
Abstract
Cryptic MHC I-associated peptides (MAPs) are produced via two mechanisms: translation of protein-coding genes in non-canonical reading frames and translation of allegedly non-coding sequences. In general, cryptic MAPs are coded by relatively short open reading frames whose translation can be regulated at the level of initiation, elongation or termination. In contrast to conventional MAPs, the processing of cryptic MAPs is frequently proteasome independent. The existence of cryptic MAPs derived from allegedly non-coding regions enlarges the scope of CD8 T cell immunosurveillance from a mere ~2% to as much as ~75% of the human genome. Considering that 99% of cancer-specific mutations are located in those allegedly non-coding regions, cryptic MAPs could furthermore represent a particularly rich source of tumor-specific antigens. However, extensive proteogenomic analyses will be required to determine the breath as well as the temporal and spatial plasticity of the cryptic MAP repertoire in normal and neoplastic cells.
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Affiliation(s)
- Céline M Laumont
- Institute for Research in Immunology and Cancer, Université de Montréal, Station Centre-Ville, PO Box 6128, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Station Centre-Ville, PO Box 6128, Montreal, QC, H3C 3J7, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Station Centre-Ville, PO Box 6128, Montreal, QC, H3C 3J7, Canada.
- Department of Medicine, Faculty of Medicine, Université de Montréal, Station Centre-Ville, PO Box 6128, Montreal, QC, H3C 3J7, Canada.
- Division of Hematology, Hôpital Maisonneuve-Rosemont, 5415 de l'Assomption Boulevard, Montreal, QC, H1T 2M4, Canada.
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28
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Martinko AJ, Truillet C, Julien O, Diaz JE, Horlbeck MA, Whiteley G, Blonder J, Weissman JS, Bandyopadhyay S, Evans MJ, Wells JA. Targeting RAS-driven human cancer cells with antibodies to upregulated and essential cell-surface proteins. eLife 2018; 7:31098. [PMID: 29359686 PMCID: PMC5796798 DOI: 10.7554/elife.31098] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 01/04/2018] [Indexed: 12/15/2022] Open
Abstract
While there have been tremendous efforts to target oncogenic RAS signaling from inside the cell, little effort has focused on the cell-surface. Here, we used quantitative surface proteomics to reveal a signature of proteins that are upregulated on cells transformed with KRASG12V, and driven by MAPK pathway signaling. We next generated a toolkit of recombinant antibodies to seven of these RAS-induced proteins. We found that five of these proteins are broadly distributed on cancer cell lines harboring RAS mutations. In parallel, a cell-surface CRISPRi screen identified integrin and Wnt signaling proteins as critical to RAS-transformed cells. We show that antibodies targeting CDCP1, a protein common to our proteomics and CRISPRi datasets, can be leveraged to deliver cytotoxic and immunotherapeutic payloads to RAS-transformed cancer cells and report for RAS signaling status in vivo. Taken together, this work presents a technological platform for attacking RAS from outside the cell.
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Affiliation(s)
- Alexander J Martinko
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Charles Truillet
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, United States
| | - Olivier Julien
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Juan E Diaz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Gordon Whiteley
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Josip Blonder
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Sourav Bandyopadhyay
- Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
| | - Michael J Evans
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
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29
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Huynh M, Pak C, Markovina S, Callander NS, Chng KS, Wuerzberger-Davis SM, Bakshi DD, Kink JA, Hematti P, Hope C, Asimakopoulos F, Rui L, Miyamoto S. Hyaluronan and proteoglycan link protein 1 (HAPLN1) activates bortezomib-resistant NF-κB activity and increases drug resistance in multiple myeloma. J Biol Chem 2017; 293:2452-2465. [PMID: 29279332 DOI: 10.1074/jbc.ra117.000667] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/22/2017] [Indexed: 01/01/2023] Open
Abstract
Nuclear factor-κB (NF-κB) is a family of transcription factors that play a key role in cell survival and proliferation in many hematological malignancies, including multiple myeloma (MM). Bortezomib, a proteasome inhibitor used in the management of MM, can inhibit both canonical and noncanonical activation of NF-κB in MM cells. However, we previously reported that a significant fraction of freshly isolated MM cells harbor bortezomib-resistant NF-κB activity. Here, we report that hyaluronan and proteoglycan link protein 1 (HAPLN1) is produced in bone marrow stromal cells from MM patients, is detected in patients' bone marrow plasma, and can activate an atypical bortezomib-resistant NF-κB pathway in MM cells. We found that this pathway involves bortezomib-resistant degradation of the inhibitor of NF-κB (IκBα), despite efficient bortezomib-mediated inhibition of proteasome activity. Moreover, HAPLN1 can also confer bortezomib-resistant survival of MM cells. We propose that HAPLN1 is a novel pathogenic factor in MM that induces an atypical NF-κB activation and thereby promotes bortezomib resistance in MM cells.
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Affiliation(s)
| | - Chorom Pak
- the Molecular and Cellular Pharmacology Graduate Program
| | - Stephanie Markovina
- the Cellular and Molecular Biology Graduate Program.,the Medical Sciences Training Program
| | - Natalie S Callander
- the University of Wisconsin Carbone Cancer Center.,the Department of Medicine
| | - Kenneth S Chng
- the McArdle Laboratory of Cancer Research, and.,the Department of Oncology, University of Wisconsin, Madison, Wisconsin 53705
| | - Shelly M Wuerzberger-Davis
- the McArdle Laboratory of Cancer Research, and.,the Department of Oncology, University of Wisconsin, Madison, Wisconsin 53705
| | | | - John A Kink
- the University of Wisconsin Carbone Cancer Center
| | - Peiman Hematti
- the University of Wisconsin Carbone Cancer Center.,the Department of Medicine
| | - Chelsea Hope
- the University of Wisconsin Carbone Cancer Center.,the Department of Medicine
| | - Fotis Asimakopoulos
- the University of Wisconsin Carbone Cancer Center.,the Department of Medicine
| | - Lixin Rui
- the University of Wisconsin Carbone Cancer Center.,the Department of Medicine
| | - Shigeki Miyamoto
- the Department of Medicine, .,the McArdle Laboratory of Cancer Research, and.,the Department of Oncology, University of Wisconsin, Madison, Wisconsin 53705
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30
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Fijalkowska D, Verbruggen S, Ndah E, Jonckheere V, Menschaert G, Van Damme P. eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs. Nucleic Acids Res 2017; 45:7997-8013. [PMID: 28541577 PMCID: PMC5570006 DOI: 10.1093/nar/gkx469] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/11/2017] [Indexed: 12/25/2022] Open
Abstract
Alternative translation initiation mechanisms such as leaky scanning and reinitiation potentiate the polycistronic nature of human transcripts. By allowing for reprogrammed translation, these mechanisms can mediate biological responses to stimuli. We combined proteomics with ribosome profiling and mRNA sequencing to identify the biological targets of translation control triggered by the eukaryotic translation initiation factor 1 (eIF1), a protein implicated in the stringency of start codon selection. We quantified expression changes of over 4000 proteins and 10 000 actively translated transcripts, leading to the identification of 245 transcripts undergoing translational control mediated by upstream open reading frames (uORFs) upon eIF1 deprivation. Here, the stringency of start codon selection and preference for an optimal nucleotide context were largely diminished leading to translational upregulation of uORFs with suboptimal start. Interestingly, genes affected by eIF1 deprivation were implicated in energy production and sensing of metabolic stress.
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Affiliation(s)
- Daria Fijalkowska
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Steven Verbruggen
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Elvis Ndah
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.,Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Veronique Jonckheere
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Gerben Menschaert
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
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31
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Liu TY, Huang HH, Wheeler D, Xu Y, Wells JA, Song YS, Wiita AP. Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics. Cell Syst 2017; 4:636-644.e9. [PMID: 28578850 DOI: 10.1016/j.cels.2017.05.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/17/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
Abstract
Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We focus on multiple myeloma cells exposed to bortezomib, a first-line chemotherapy and proteasome inhibitor. In the absence of drug effects, we found that direct measurement of protein synthesis by pSILAC correlated well with indirect measurement of synthesis from ribosome footprint density. This correlation, however, broke down under bortezomib-induced stress. By developing a statistical model integrating longitudinal proteomic and mRNA-sequencing measurements, we found that proteomics could directly detect global alterations in translational rate caused by bortezomib; these changes are not detectable by ribosomal profiling alone. Further, by incorporating pSILAC data into a gene expression model, we predict cell-stress specific proteome remodeling events. These results demonstrate that pSILAC provides an important complement to ribosome profiling in measuring proteome dynamics.
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Affiliation(s)
- Tzu-Yu Liu
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA; Departments of Mathematics and Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hector H Huang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Diamond Wheeler
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yichen Xu
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA; Departments of Mathematics and Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA.
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32
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Caspases and their substrates. Cell Death Differ 2017; 24:1380-1389. [PMID: 28498362 DOI: 10.1038/cdd.2017.44] [Citation(s) in RCA: 486] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 12/14/2022] Open
Abstract
, or for pyroptosis, gasdermin D. For the most part, it appears that cleavage events function cooperatively in the cell death process to generate a proteolytic synthetic lethal outcome. In contrast to apoptosis, far less is known about caspase biology in non-apoptotic cellular processes, such as cellular remodeling, including which caspases are activated, the mechanisms of their activation and deactivation, and the key substrate targets. Here we survey the progress made in global identification of caspase substrates using proteomics and the exciting new avenues these studies have opened for understanding the molecular logic of substrate cleavage in apoptotic and non-apoptotic processes.
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33
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Calvo SE, Julien O, Clauser KR, Shen H, Kamer KJ, Wells JA, Mootha VK. Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast. Mol Cell Proteomics 2017; 16:512-523. [PMID: 28122942 DOI: 10.1074/mcp.m116.063818] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 01/06/2017] [Indexed: 01/08/2023] Open
Abstract
The majority of mitochondrial proteins are encoded in the nuclear genome, translated in the cytoplasm, and directed to the mitochondria by an N-terminal presequence that is cleaved upon import. Recently, N-proteome catalogs have been generated for mitochondria from yeast and from human U937 cells. Here, we applied the subtiligase method to determine N-termini for 327 proteins in mitochondria isolated from mouse liver and kidney. Comparative analysis between mitochondrial N-termini from mouse, human, and yeast proteins shows that whereas presequences are poorly conserved at the sequence level, other presequence properties are extremely conserved, including a length of ∼20-60 amino acids, a net charge between +3 to +6, and the presence of stabilizing amino acids at the N-terminus of mature proteins that follow the N-end rule from bacteria. As in yeast, ∼80% of mouse presequence cleavage sites match canonical motifs for three mitochondrial peptidases (MPP, Icp55, and Oct1), whereas the remainder do not match any known peptidase motifs. We show that mature mitochondrial proteins often exist with a spectrum of N-termini, consistent with a model of multiple cleavage events by MPP and Icp55. In addition to analysis of canonical targeting presequences, our N-terminal dataset allows the exploration of other cleavage events and provides support for polypeptide cleavage into two distinct enzymes (Hsd17b4), protein cleavages key for signaling (Oma1, Opa1, Htra2, Mavs, and Bcs2l13), and in several cases suggests novel protein isoforms (Scp2, Acadm, Adck3, Hsdl2, Dlst, and Ogdh). We present an integrated catalog of mammalian mitochondrial N-termini that can be used as a community resource to investigate individual proteins, to elucidate mechanisms of mammalian mitochondrial processing, and to allow researchers to engineer tags distally to the presequence cleavage.
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Affiliation(s)
- Sarah E Calvo
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114; .,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115.,¶Broad Institute, Cambridge, Massachusetts 02141
| | | | | | - Hongying Shen
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Kimberli J Kamer
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - James A Wells
- **Departments of Pharmaceutical Chemistry and.,§§Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143
| | - Vamsi K Mootha
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
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34
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Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ. Interactome disassembly during apoptosis occurs independent of caspase cleavage. Mol Syst Biol 2017; 13:906. [PMID: 28082348 PMCID: PMC5293159 DOI: 10.15252/msb.20167067] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Protein-protein interaction networks (interactomes) define the functionality of all biological systems. In apoptosis, proteolysis by caspases is thought to initiate disassembly of protein complexes and cell death. Here we used a quantitative proteomics approach, protein correlation profiling (PCP), to explore changes in cytoplasmic and mitochondrial interactomes in response to apoptosis initiation as a function of caspase activity. We measured the response to initiation of Fas-mediated apoptosis in 17,991 interactions among 2,779 proteins, comprising the largest dynamic interactome to date. The majority of interactions were unaffected early in apoptosis, but multiple complexes containing known caspase targets were disassembled. Nonetheless, proteome-wide analysis of proteolytic processing by terminal amine isotopic labeling of substrates (TAILS) revealed little correlation between proteolytic and interactome changes. Our findings show that, in apoptosis, significant interactome alterations occur before and independently of caspase activity. Thus, apoptosis initiation includes a tight program of interactome rearrangement, leading to disassembly of relatively few, select complexes. These early interactome alterations occur independently of cleavage of these protein by caspases.
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Affiliation(s)
- Nichollas E Scott
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Lindsay D Rogers
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Anna Prudova
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Nat F Brown
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Nikolaus Fortelny
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada .,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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35
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Rovozzo R, Korza G, Baker MW, Li M, Bhattacharyya A, Barbarese E, Carson JH. CGG Repeats in the 5'UTR of FMR1 RNA Regulate Translation of Other RNAs Localized in the Same RNA Granules. PLoS One 2016; 11:e0168204. [PMID: 28005950 PMCID: PMC5179066 DOI: 10.1371/journal.pone.0168204] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/28/2016] [Indexed: 01/24/2023] Open
Abstract
CGG repeats in the 5’UTR of Fragile X Mental Retardation 1 (FMR1) RNA mediate RNA localization and translation in granules. Large expansions of CGG repeats (> 200 repeats) in FMR1, referred to as full mutations, are associated with fragile X syndrome (FXS). Smaller expansions (55–200 repeats), referred to as premutations, are associated with fragile X tremor ataxia syndrome (FXTAS) and fragile X premature ovarian insufficiency (FXPOI). TMPyP4 is a porphyrin ring compound that destabilizes CGG repeat RNA secondary structure. Here we show that exogenous CGG repeat RNA by itself, lacking the FMRP ORF, microinjected into hippocampal neurons is localized in RNA granules and inhibits translation of ARC RNA, which is localized in the same granules. TMPyP4 rescues translation of ARC RNA in granules. We also show that in human premutation fibroblasts with endogenous CGG repeat expansions in the FMR1 gene, translation of ARC RNA is inhibited and calcium homeostasis is disrupted and both phenotypes are rescued by TMPyP4. Inhibition of granule translation by expanded CGG repeats and rescue of granule translation by TMPy4, represent potential pathogenic mechanism and therapeutic strategy, respectively, for FXTAS and FXPOI.
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Affiliation(s)
- René Rovozzo
- Center for Cell Analysis and Modeling, UConn Health, Farmington, Connecticut, United States of America
| | - George Korza
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, United States of America
| | - Mei W. Baker
- Departments of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin State Laboratory of Hygiene, Newborn Screening Laboratory, Madison, Wisconsin, United States of America
| | - Meng Li
- Waisman Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Anita Bhattacharyya
- Waisman Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Elisa Barbarese
- Department of Neuroscience, UConn Health, Farmington, Connecticut, United States of America
| | - John H. Carson
- Center for Cell Analysis and Modeling, UConn Health, Farmington, Connecticut, United States of America
- * E-mail:
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Profilin potentiates chemotherapeutic agents mediated cell death via suppression of NF-κB and upregulation of p53. Apoptosis 2016; 21:502-13. [PMID: 26842845 DOI: 10.1007/s10495-016-1222-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The molecular mechanism by which Profilin acts as a tumor suppressor is still unclear. Several chemotherapeutic agents, used till date either have unfavorable side effects or acquired resistance in tumor cells. Our findings show that Profilin enhances cell death mediated by several chemotherapeutic-agents. The activation of NF-κB and its dependent genes, mediated by paclitaxel and vinblastine, was completely inhibited in Profilin overexpressing cells. This inhibition was due to the Profilin mediated attenuation of IκBα degradation, thereby preventing p65 nuclear translocation and low NF-κB DNA binding activity.Moreover, Profilin increases level of p53 in the presence of known inducers, such as doxorubicin, vinblastine, and benzofuran. This increased p53 level leads to enhanced cell death as indicated by activation of caspases 3, 8, 9, which results in cleavage of PARP.Furthermore, knocking down of p53 in Profilin overexpressing cells leads to decreased cell death. Ectopic expression of Profilin in HCT116 p53 knock out cells showed lesser cell death as compared to the HCT116 p53 wild type cells. For the first time, we provide evidences, which suggest that Profilin synergizes with chemotherapeutic drugs to induce tumor cell death by regulating NF-κB and p53. Thus, modulation of Profilin may be a useful strategy for effective combination therapy.
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Sherbenou DW, Aftab BT, Su Y, Behrens CR, Wiita A, Logan AC, Acosta-Alvear D, Hann BC, Walter P, Shuman MA, Wu X, Atkinson JP, Wolf JL, Martin TG, Liu B. Antibody-drug conjugate targeting CD46 eliminates multiple myeloma cells. J Clin Invest 2016; 126:4640-4653. [PMID: 27841764 DOI: 10.1172/jci85856] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 10/06/2016] [Indexed: 12/21/2022] Open
Abstract
Multiple myeloma is incurable by standard approaches because of inevitable relapse and development of treatment resistance in all patients. In our prior work, we identified a panel of macropinocytosing human monoclonal antibodies against CD46, a negative regulator of the innate immune system, and constructed antibody-drug conjugates (ADCs). In this report, we show that an anti-CD46 ADC (CD46-ADC) potently inhibited proliferation in myeloma cell lines with little effect on normal cells. CD46-ADC also potently eliminated myeloma growth in orthometastatic xenograft models. In primary myeloma cells derived from bone marrow aspirates, CD46-ADC induced apoptosis and cell death, but did not affect the viability of nontumor mononuclear cells. It is of clinical interest that the CD46 gene resides on chromosome 1q, which undergoes genomic amplification in the majority of relapsed myeloma patients. We found that the cell surface expression level of CD46 was markedly higher in patient myeloma cells with 1q gain than in those with normal 1q copy number. Thus, genomic amplification of CD46 may serve as a surrogate for target amplification that could allow patient stratification for tailored CD46-targeted therapy. Overall, these findings indicate that CD46 is a promising target for antibody-based treatment of multiple myeloma, especially in patients with gain of chromosome 1q.
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Norris EL, Headlam MJ, Dave KA, Smith DD, Bukreyev A, Singh T, Jayakody BA, Chappell KJ, Collins PL, Gorman JJ. Proteoform-Specific Insights into Cellular Proteome Regulation. Mol Cell Proteomics 2016; 15:3297-3320. [PMID: 27451424 PMCID: PMC5054351 DOI: 10.1074/mcp.o116.058438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Indexed: 01/29/2023] Open
Abstract
Knowledge regarding compositions of proteomes at the proteoform level enhances insights into cellular phenotypes. A strategy is described herein for discovery of proteoform-specific information about cellular proteomes. This strategy involved analysis of data obtained by bottom-up mass spectrometry of multiple protein OGE separations on a fraction by fraction basis. The strategy was exemplified using five matched sets of lysates of uninfected and human respiratory syncytial virus-infected A549 cells. Template matching demonstrated that 67.3% of 10475 protein profiles identified focused to narrow pI windows indicative of efficacious focusing. Furthermore, correlation between experimental and theoretical pI gradients indicated reproducible focusing. Based on these observations a proteoform profiling strategy was developed to identify proteoforms, detect proteoform diversity and discover potential proteoform regulation. One component of this strategy involved examination of the focusing profiles for protein groups. A novel concordance analysis facilitated differentiation between proteoforms, including proteoforms generated by alternate splicing and proteolysis. Evaluation of focusing profiles and concordance analysis were applicable to cells from a single and/or multiple biological states. Statistical analyses identified proteoform variation between biological states. Regulation relevant to cellular responses to human respiratory syncytial virus was revealed. Western blotting and Protomap analyses validated the proteoform regulation. Discovery of STAT1, WARS, MX1, and HSPB1 proteoform regulation by human respiratory syncytial virus highlighted the impact of the profiling strategy. Novel truncated proteoforms of MX1 were identified in infected cells and phosphorylation driven regulation of HSPB1 proteoforms was correlated with infection. The proteoform profiling strategy is generally applicable to investigating interactions between viruses and host cells and the analysis of other biological systems.
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Affiliation(s)
| | | | | | - David D Smith
- §Statistics Unit, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Alexander Bukreyev
- ¶Respiratory Virus Section, Laboratory of Infectious Diseases, National Institute for Allergy and Infectious Diseases, NIH, Bethesda, Maryland, and
| | | | | | - Keith J Chappell
- ‖School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Peter L Collins
- ¶Respiratory Virus Section, Laboratory of Infectious Diseases, National Institute for Allergy and Infectious Diseases, NIH, Bethesda, Maryland, and
| | - Jeffrey J Gorman
- From the ‡Protein Discovery Centre and ‖School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
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Pérez-Garijo A, Steller H. Spreading the word: non-autonomous effects of apoptosis during development, regeneration and disease. Development 2016; 142:3253-62. [PMID: 26443630 DOI: 10.1242/dev.127878] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Apoptosis, in contrast to other forms of cell death such as necrosis, was originally regarded as a 'silent' mechanism of cell elimination designed to degrade the contents of doomed cells. However, during the past decade it has become clear that apoptotic cells can produce diverse signals that have a profound impact on neighboring cells and tissues. For example, apoptotic cells can release factors that influence the proliferation and survival of adjacent tissues. Apoptosis can also affect tissue movement and morphogenesis by modifying tissue tension in surrounding cells. As we review here, these findings reveal unexpected roles for apoptosis in tissue remodeling during development, as well as in regeneration and cancer.
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Affiliation(s)
- Ainhoa Pérez-Garijo
- Strang Laboratory of Apoptosis and Cancer Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Hermann Steller
- Strang Laboratory of Apoptosis and Cancer Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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Baharara J, Amini E, Namvar F. Evaluation of the Anti-proliferative Effects of Ophiocoma erinaceus Methanol Extract Against Human Cervical Cancer Cells. Avicenna J Med Biotechnol 2016; 8:29-35. [PMID: 26855733 PMCID: PMC4717464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
BACKGROUND Marine organisms provide appreciable source of novel bioactive compounds with pharmacological potential. There is little information in correlation with anti-cancer activities of brittle star. In the present study, anti-neoplastic efficacy of Ophiocoma erinaceus methanol extract against human cervical cancer cells was investigated. METHODS The HeLa cells were cultured and exposed to brittle star methanol extract for 24 and 48 hr. The anti-proliferative properties were examined by MTT assay and the type of cell death induced was evaluated through morphological changes, flow cytometry, Annexin kit and caspase assay. To assess the anti-metastatic activity, wound healing assay was conducted and photographs were taken from the scratched areas. Further, to understand molecular mechanism of cell apoptosis, the expression of Bax was evaluated. RESULTS The morphological analysis and MTT assay exhibited that the brittle star methanol extract can exert dose dependent inhibitory effect on cells viability (IC50, 50 μg/ml). Flow cytometry and fluorescence microscopy demonstrated increment of sub-G1 peak, early and late apoptosis in HeLa treated cells. Wound healing migration assay showed that brittle star extract has anti-neoplastic efficacy by inhibiting cell migration. Caspase assay and RT-PCR analysis revealed that brittle star methanol extract induced caspase dependent apoptosis in HeLa cells through up-regulation of caspase-3 followed by up-regulation of Bax gene which is a hallmark of intrinsic pathway recruitment. CONCLUSION These results represented further insights into the chemopreventive potential of brittle star as a valuable source of unknown therapeutic agents against human cervical cancer.
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Affiliation(s)
- Javad Baharara
- Department of Biology, Research Center for Animal Development Applied Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran,Corresponding author: Javad Baharara, Ph.D., Department of Biology, Research Center for Animal Developmental Applied Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran, Tel: +98 511 8437092, Fax: +98 511 8437092, E-mail:
| | - Elaheh Amini
- Department of Animal Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Farideh Namvar
- Department of Biology, Research Center for Animal Development Applied Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran,Institute of Tropical Forestry and Forest Products, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Hart JR, Roberts TC, Weinberg MS, Morris KV, Vogt PK. MYC regulates the non-coding transcriptome. Oncotarget 2015; 5:12543-54. [PMID: 25587025 PMCID: PMC4350361 DOI: 10.18632/oncotarget.3033] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 01/17/2023] Open
Abstract
Using RNA-seq (RNA sequencing) of ribosome-depleted RNA, we have identified 1,273 lncRNAs (long non-coding RNAs) in P493-6 human B-cells. Of these, 534 are either up- or downregulated in response to MYC overexpression. An increase in MYC occupancy near their TSS (transcription start sites) was observed for MYC-responsive lncRNAs suggesting these are direct MYC targets. MYC binds to the same TSS across several cell lines, but the number of TSS bound depends on cellular MYC levels and increases with higher MYC concentrations. Despite this concordance in promoter binding, a majority of expressed lncRNAs are specific for one cell line, suggesting a determinant role of additional, possibly differentiation-specific factors in the activity of MYC-bound lncRNA promoters. A significant fraction of the lncRNA transcripts lack polyadenylation. The RNA-seq data were confirmed on eight selected lncRNAs by NRO (nuclear run-on) and RT-qPCR (quantitative reverse transcription PCR).
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Affiliation(s)
- Jonathan R Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Thomas C Roberts
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, WITS, South Africa
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. School of Biotechnology and Biomedical Sciences, University of New South Wales, NSW, Australia
| | - Peter K Vogt
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
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42
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Chung BY, Hardcastle TJ, Jones JD, Irigoyen N, Firth AE, Baulcombe DC, Brierley I. The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis. RNA (NEW YORK, N.Y.) 2015; 21:1731-45. [PMID: 26286745 PMCID: PMC4574750 DOI: 10.1261/rna.052548.115] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/23/2015] [Indexed: 05/19/2023]
Abstract
Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but uses duplex-specific nuclease (DSN) as a convenient, species-independent way to reduce rRNA contamination. We show that DSN-based depletion compares favorably with other commonly used rRNA depletion strategies and introduces little bias. The profiling protocol typically produces high levels of triplet periodicity, facilitating the detection of coding sequences, including upstream, downstream, and overlapping open reading frames (ORFs) and an alternative ribosome conformation evident during termination of protein synthesis. In addition, we provide a software package that presents a set of methods for parsing ribosomal profiling data from multiple samples, aligning reads to coding sequences, inferring alternative ORFs, and plotting average and transcript-specific aspects of the data. Methods are also provided for extracting the data in a form suitable for differential analysis of translation and translational efficiency.
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Affiliation(s)
- Betty Y Chung
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Joshua D Jones
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
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Shah SP, Lonial S, Boise LH. When Cancer Fights Back: Multiple Myeloma, Proteasome Inhibition, and the Heat-Shock Response. Mol Cancer Res 2015; 13:1163-73. [PMID: 26013169 DOI: 10.1158/1541-7786.mcr-15-0135] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/13/2015] [Indexed: 01/01/2023]
Abstract
Multiple myeloma is a plasma cell malignancy with an estimated 26,850 new cases and 11,240 deaths in 2015 in the United States. Two main classes of agents are the mainstays of therapy-proteasome inhibitors (PI) and immunomodulatory drugs (IMiD). Other new targets are emerging rapidly, including monoclonal antibodies and histone deacetylase (HDAC) inhibitors. These therapeutic options have greatly improved overall survival, but currently only 15% to 20% of patients experience long-term progression-free survival or are cured. Therefore, improvement in treatment options is needed. One potential means of improving clinical options is to target resistance mechanisms for current agents. For example, eliminating the cytoprotective heat-shock response that protects myeloma cells from proteasome inhibition may enhance PI-based therapies. The transcription factor heat-shock factor 1 (HSF1) is the master regulator of the heat-shock response. HSF1 is vital in the proteotoxic stress response, and its activation is controlled by posttranslational modifications (PTM). This review details the mechanisms of HSF1 regulation and discusses leveraging that regulation to enhance PI activity.
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Affiliation(s)
- Shardule P Shah
- Department of Hematology and Medical Oncology, Winship, Cancer Institute of Emory University and the Emory University School of Medicine, Atlanta, Georgia
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship, Cancer Institute of Emory University and the Emory University School of Medicine, Atlanta, Georgia
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, Winship, Cancer Institute of Emory University and the Emory University School of Medicine, Atlanta, Georgia. Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia.
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44
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Andreev DE, O'Connor PBF, Zhdanov AV, Dmitriev RI, Shatsky IN, Papkovsky DB, Baranov PV. Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes. Genome Biol 2015; 16:90. [PMID: 25943107 PMCID: PMC4419486 DOI: 10.1186/s13059-015-0651-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/13/2015] [Indexed: 01/10/2023] Open
Abstract
Background Oxygen and glucose metabolism play pivotal roles in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) during ischemia and stroke results in extensive tissue injury and cell death. Results Using time-resolved ribosome profiling, we assess gene expression levels in a neural cell line, PC12, during the first hour of OGD. The most substantial alterations are seen to occur within the first 20 minutes of OGD. While transcription of only 100 genes is significantly altered during one hour of OGD, the translation response affects approximately 3,000 genes. This response involves reprogramming of initiation and elongation rates, as well as the stringency of start codon recognition. Genes involved in oxidative phosphorylation are most affected. Detailed analysis of ribosome profiles reveals salient alterations of ribosome densities on individual mRNAs. The mRNA-specific alterations include increased translation of upstream open reading frames, site-specific ribosome pauses, and production of alternative protein isoforms with amino-terminal extensions. Detailed analysis of ribosomal profiles also reveals six mRNAs with translated ORFs occurring downstream of annotated coding regions and two examples of dual coding mRNAs, where two protein products are translated from the same long segment of mRNA, but in two different frames. Conclusions These findings uncover novel regulatory mechanisms of translational response to OGD in mammalian cells that are different from the classical pathways such as hypoxia inducible factor (HIF) signaling, while also revealing sophisticated organization of protein coding information in certain genes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0651-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dmitry E Andreev
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Patrick B F O'Connor
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland.
| | - Alexander V Zhdanov
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland.
| | - Ruslan I Dmitriev
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland.
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Dmitri B Papkovsky
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland. .,Institute of Biomedical Chemistry, Pogodinskaya street, Moscow, 119121, Russia.
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland.
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Popp MW, Maquat LE. Attenuation of nonsense-mediated mRNA decay facilitates the response to chemotherapeutics. Nat Commun 2015; 6:6632. [PMID: 25808464 PMCID: PMC4375787 DOI: 10.1038/ncomms7632] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 02/13/2015] [Indexed: 12/27/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) limits the production of aberrant mRNAs containing a premature termination codon and also controls the levels of endogenous transcripts. Here we show that when human cells are treated with clinically used chemotherapeutic compounds, NMD activity declines partly as a result of the proteolytic production of a dominant-interfering form of the key NMD factor UPF1. Production of cleaved UPF1 functions to upregulate genes involved in the response to apoptotic stresses. The biological consequence is the promotion of cell death. Combined exposure of cells to a small-molecule inhibitor of NMD, NMDI-1, and the chemotherapeutic doxorubicin leads to enhanced cell death, while inhibiting UPF1 cleavage protects cells from doxorubicin challenge. We propose a model to explain why the expression levels of genes producing mRNAs of diverse structure that encode proteins of diverse function are under the purview of NMD.
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Affiliation(s)
- Maximilian W Popp
- 1] Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA [2] Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- 1] Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA [2] Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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46
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Yan CM, Chai EQ, Cai HY, Miao GY, Ma W. Oleuropein induces apoptosis via activation of caspases and suppression of phosphatidylinositol 3-kinase/protein kinase B pathway in HepG2 human hepatoma cell line. Mol Med Rep 2015; 11:4617-24. [PMID: 25634350 DOI: 10.3892/mmr.2015.3266] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 12/12/2014] [Indexed: 12/20/2022] Open
Abstract
Oleuropein is a polyphenol, that is found in extra‑virgin olive oil. Previous studies have shown that oleuropein inhibits cell proliferation and induces apoptosis in breast cancer, colorectal cancer and thyroid cancer. The aim of the present study was to investigate the effects of oleuropein in hepatocellular carcinoma (HCC) cells. The results of Cell Counting Kit 8 and flow cytometric analysis indicated that oleuropein effectively inhibited cell viability and induced apoptosis in HepG2 human hepatoma cells in a dose‑dependent manner, through activation of the caspase pathway. Proapoptotic Bcl‑2 family members, BAX and Bcl‑2, were involved in oleuropein‑induced apoptosis. The phosphatidylinositol 3‑kinase/protein kinase B (PI3K/AKT) signaling pathway was also shown to be involved in this process. Oleuropein was demonstrated to suppress the expression of activated AKT. In addition, AKT overexpression promoted cell survival following treatment with oleuropein, while inhibition of AKT promoted cell death. Furthermore, the data demonstrated that oleuropein induces the production of reactive oxygen species (ROS) and that the function of oleuropein is, at least partially, ROS‑dependent. These results suggest that oleuropein may be a promising novel chemotherapeutic agent in hepatocellular carcinoma.
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Affiliation(s)
- Chun-Mei Yan
- Department of Radiotherapy Oncology, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Er-Qing Chai
- Cerebrovascular Diseases Center, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Hong-Yi Cai
- Department of Radiotherapy Oncology, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Guo-Ying Miao
- Department of Radiotherapy Oncology, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Wen Ma
- Department of Radiotherapy Oncology, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
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47
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Gawron D, Gevaert K, Van Damme P. The proteome under translational control. Proteomics 2014; 14:2647-62. [PMID: 25263132 DOI: 10.1002/pmic.201400165] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/21/2014] [Accepted: 09/23/2014] [Indexed: 02/02/2023]
Abstract
A single eukaryotic gene can give rise to a variety of protein forms (proteoforms) as a result of genetic variation and multilevel regulation of gene expression. In addition to alternative splicing, an increasing line of evidence shows that alternative translation contributes to the overall complexity of proteomes. Identifying the repertoire of proteins and micropeptides expressed by alternative selection of (near-)cognate translation initiation sites and different reading frames however remains challenging with contemporary proteomics. MS-enabled identification of proteoforms is expected to benefit from transcriptome and translatome data by the creation of customized and sample-specific protein sequence databases. Here, we focus on contemporary integrative omics approaches that complement proteomics with DNA- and/or RNA-oriented technologies to elucidate the mechanisms of translational control. Together, these technologies enable to map the translation (initiation) landscape and more comprehensively define the inventory of proteoforms raised upon alternative translation, thus assisting in the (re-)annotation of genomes.
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Affiliation(s)
- Daria Gawron
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
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48
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Julien O, Kampmann M, Bassik MC, Zorn JA, Venditto VJ, Shimbo K, Agard NJ, Shimada K, Rheingold AL, Stockwell BR, Weissman JS, Wells JA. Unraveling the mechanism of cell death induced by chemical fibrils. Nat Chem Biol 2014; 10:969-76. [PMID: 25262416 PMCID: PMC4201873 DOI: 10.1038/nchembio.1639] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/20/2014] [Indexed: 12/20/2022]
Abstract
We previously discovered a small-molecule inducer of cell death, named 1541, that noncovalently self-assembles into chemical fibrils ('chemi-fibrils') and activates procaspase-3 in vitro. We report here that 1541-induced cell death is caused by the fibrillar rather than the soluble form of the drug. A short hairpin RNA screen reveals that knockdown of genes involved in endocytosis, vesicle trafficking and lysosomal acidification causes partial 1541 resistance. We confirm the role of these pathways using pharmacological inhibitors. Microscopy shows that the fluorescent chemi-fibrils accumulate in punctae inside cells that partially colocalize with lysosomes. Notably, the chemi-fibrils bind and induce liposome leakage in vitro, suggesting they may do the same in cells. The chemi-fibrils induce extensive proteolysis including caspase substrates, yet modulatory profiling reveals that chemi-fibrils form a distinct class from existing inducers of cell death. The chemi-fibrils share similarities with proteinaceous fibrils and may provide insight into their mechanism of cellular toxicity.
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Affiliation(s)
- Olivier Julien
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA
| | - Martin Kampmann
- 1] Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA. [2] Howard Hughes Medical Institute, University of California-San Francisco, San Francisco, California, USA
| | - Michael C Bassik
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA
| | - Julie A Zorn
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA
| | - Vincent J Venditto
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, California, USA
| | - Kazutaka Shimbo
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA
| | - Nicholas J Agard
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA
| | - Kenichi Shimada
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Arnold L Rheingold
- Department of Chemistry, University of California-San Diego, San Diego, California, USA
| | - Brent R Stockwell
- 1] Department of Biological Sciences, Columbia University, New York, New York, USA. [2] Department of Chemistry, Columbia University, New York, New York, USA. [3] Howard Hughes Medical Institute, Columbia University, New York, New York, USA
| | - Jonathan S Weissman
- 1] Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA. [2] Howard Hughes Medical Institute, University of California-San Francisco, San Francisco, California, USA
| | - James A Wells
- 1] Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA. [2] Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA
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49
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Han L, Yuan Y, Zheng S, Yang Y, Li J, Edgerton ME, Diao L, Xu Y, Verhaak RGW, Liang H. The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes. Nat Commun 2014; 5:3963. [PMID: 24999802 PMCID: PMC4339277 DOI: 10.1038/ncomms4963] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/13/2014] [Indexed: 12/30/2022] Open
Abstract
Although individual pseudogenes have been implicated in tumor biology, the biomedical significance and clinical relevance of pseudogene expression have not been assessed in a systematic way. Here we generate pseudogene expression profiles in 2,808 patient samples of seven cancer types from The Cancer Genome Atlas RNA-seq data using a newly developed computational pipeline. Supervised analysis reveals a significant number of pseudogenes differentially expressed among established tumor subtypes; and pseudogene expression alone can accurately classify the major histological subtypes of endometrial cancer. Across cancer types, the tumor subtypes revealed by pseudogene expression show extensive and strong concordance with the subtypes defined by other molecular data. Strikingly, in kidney cancer, the pseudogene-expression subtypes not only significantly correlate with patient survival, but also help stratify patients in combination with clinical variables. Our study highlights the potential of pseudogene expression analysis as a new paradigm for investigating cancer mechanisms and discovering prognostic biomarkers.
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Affiliation(s)
- Leng Han
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA
| | - Yuan Yuan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Siyuan Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA
| | - Yang Yang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.,Division of Biostatistics, The University of Texas Health Science Center at Houston, School of Public Health, Houston, TX 77030, USA
| | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA
| | - Mary E Edgerton
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA
| | - Yanxun Xu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA
| | - Roeland G W Verhaak
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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50
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Stickel S, Gomes N, Su TT. The Role of Translational Regulation in Survival after Radiation Damage; an Opportunity for Proteomics Analysis. Proteomes 2014; 2:272-290. [PMID: 26269784 PMCID: PMC4530795 DOI: 10.3390/proteomes2020272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 05/31/2014] [Accepted: 06/04/2014] [Indexed: 12/20/2022] Open
Abstract
In this review, we will summarize the data from different model systems that illustrate the need for proteome-wide analyses of the biological consequences of ionizing radiation (IR). IR remains one of three main therapy choices for oncology, the others being surgery and chemotherapy. Understanding how cells and tissues respond to IR is essential for improving therapeutic regimes against cancer. Numerous studies demonstrating the changes in the transcriptome following exposure to IR, in diverse systems, can be found in the scientific literature. However, the limitation of our knowledge is illustrated by the fact that the number of transcripts that change after IR exposure is approximately an order of magnitude lower than the number of transcripts that re-localize to or from ribosomes under similar conditions. Furthermore, changes in the post-translational modifications of proteins (phosphorylation, acetylation as well as degradation) are profoundly important for the cellular response to IR. These considerations make proteomics a highly suitable tool for mechanistic studies of the effect of IR. Strikingly such studies remain outnumbered by those utilizing proteomics for diagnostic purposes such as the identification of biomarkers for the outcome of radiation therapy. Here we will discuss the role of the ribosome and translational regulation in the survival and preservation of cells and tissues after exposure to ionizing radiation. In doing so we hope to provide a strong incentive for the study of proteome-wide changes following IR exposure.
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Affiliation(s)
- Stefanie Stickel
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; E-Mails: (S.S.); (N.G.)
| | - Nathan Gomes
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; E-Mails: (S.S.); (N.G.)
- SuviCa, Inc. P O Box 3131, Boulder, CO 80301, USA
| | - Tin Tin Su
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; E-Mails: (S.S.); (N.G.)
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