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Niederkorn M, Ishikawa C, M. Hueneman K, Bartram J, Stepanchick E, R. Bennett J, E. Culver-Cochran A, Bolanos LC, Uible E, Choi K, Wunderlich M, Perentesis JP, M. Chlon T, Filippi MD, Starczynowski DT. The deubiquitinase USP15 modulates cellular redox and is a therapeutic target in acute myeloid leukemia. Leukemia 2022; 36:438-451. [PMID: 34465865 PMCID: PMC8807387 DOI: 10.1038/s41375-021-01394-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023]
Abstract
Ubiquitin-specific peptidase 15 (USP15) is a deubiquitinating enzyme implicated in critical cellular and oncogenic processes. We report that USP15 mRNA and protein are overexpressed in human acute myeloid leukemia (AML) as compared to normal hematopoietic progenitor cells. This high expression of USP15 in AML correlates with KEAP1 protein and suppression of NRF2. Knockdown or deletion of USP15 in human and mouse AML models significantly impairs leukemic progenitor function and viability and de-represses an antioxidant response through the KEAP1-NRF2 axis. Inhibition of USP15 and subsequent activation of NRF2 leads to redox perturbations in AML cells, coincident with impaired leukemic cell function. In contrast, USP15 is dispensable for human and mouse normal hematopoietic cells in vitro and in vivo. A preclinical small-molecule inhibitor of USP15 induced the KEAP1-NRF2 axis and impaired AML cell function, suggesting that targeting USP15 catalytic function can suppress AML. Based on these findings, we report that USP15 drives AML cell function, in part, by suppressing a critical oxidative stress sensor mechanism and permitting an aberrant redox state. Furthermore, we postulate that inhibition of USP15 activity with small molecule inhibitors will selectively impair leukemic progenitor cells by re-engaging homeostatic redox responses while sparing normal hematopoiesis.
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Affiliation(s)
- Madeline Niederkorn
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Chiharu Ishikawa
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Kathleen M. Hueneman
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - James Bartram
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Emily Stepanchick
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Joshua R. Bennett
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Ashley E. Culver-Cochran
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Lyndsey C. Bolanos
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Emma Uible
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Kwangmin Choi
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Mark Wunderlich
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - John P. Perentesis
- grid.239573.90000 0000 9025 8099Division of Oncology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Timothy M. Chlon
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Marie-Dominique Filippi
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Daniel T. Starczynowski
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
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Kriss CL, Duro N, Nadeau OW, Guergues J, Chavez-Chiang O, Culver-Cochran AE, Chaput D, Varma S, Stevens SM. Site-specific identification and validation of hepatic histone nitration in vivo: Implications for alcohol-induced liver injury. J Mass Spectrom 2021; 56:e4713. [PMID: 33942435 DOI: 10.1002/jms.4713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/29/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Oxidative and nitrative stress have been implicated in the molecular mechanisms underlying a variety of biological processes and disease states including cancer, aging, cardiovascular disease, neurological disorders, diabetes, and alcohol-induced liver injury. One marker of nitrative stress is the formation of 3-nitrotyrosine, or protein tyrosine nitration (PTN), which has been observed during inflammation and tissue injury; however, the role of PTN in the progression or possibly the pathogenesis of disease is still unclear. We show in a model of alcohol-induced liver injury that an increase in PTN occurs in hepatocyte nuclei within the liver of wild-type male C57BL/6J mice following chronic ethanol exposure (28 days). High-resolution mass spectrometric analysis of isolated hepatic nuclei revealed several novel sites of tyrosine nitration on histone proteins. Histone nitration sites were validated by tandem mass spectrometry (MS/MS) analysis of representative synthetic nitropeptides equivalent in sequence to the respective nitrotyrosine sites identified in vivo. We further investigated the potential structural impact of the novel histone H3 Tyr41 (H3Y41) nitration site identified using molecular dynamics (MD) simulations. MD simulations of the nitrated and non-nitrated forms of histone H3Y41 showed significant structural changes at the DNA interface upon H3Y41 nitration. The results from this study suggest that, in addition to other known post-translational modifications that occur on histone proteins (e.g., acetylation and methylation), PTN could induce chromatin structural changes, possibly affecting gene transcription processes associated with the development of alcohol-induced liver injury.
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Affiliation(s)
- Crystina L Kriss
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA
- Department of Cardiovascular Regeneration, Houston Methodist Research Institute, 6607 Bertner Ave, Houston, TX, 77030, USA
| | - Nalvi Duro
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA
| | - Owen W Nadeau
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Dr, Colchester, VT, 05446, USA
| | - Jennifer Guergues
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Dr, Colchester, VT, 05446, USA
- MSRC Proteomics Core Laboratory, Vanderbilt University, Medical Research Building III, Nashville, TN, 37232, USA
| | - Omar Chavez-Chiang
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB-3, Tampa, FL, 33612, USA
| | - Ashley E Culver-Cochran
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Dale Chaput
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA
| | - Sameer Varma
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA
| | - Stanley M Stevens
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA
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Smith MA, Culver-Cochran AE, Adelman ER, Rhyasen GW, Ma A, Figueroa ME, Starczynowski DT. TNFAIP3 Plays a Role in Aging of the Hematopoietic System. Front Immunol 2020; 11:536442. [PMID: 33224133 PMCID: PMC7670064 DOI: 10.3389/fimmu.2020.536442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 10/09/2020] [Indexed: 12/22/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPC) experience a functional decline in response to chronic inflammation or aging. Haploinsufficiency of A20, or TNFAIP3, an innate immune regulator, is associated with a variety of autoimmune, inflammatory, and hematologic malignancies. Based on a prior analysis of epigenomic and transcriptomic changes during normal human aging, we find that the expression of A20 is significantly reduced in aged HSPC as compared to young HSPC. Here, we show that the partial reduction of A20 expression in young HSPC results in characteristic features of aging. Specifically, heterozygous deletion of A20 in hematopoietic cells resulted in expansion of the HSPC pool, reduced HSPC fitness, and myeloid-biased hematopoiesis. These findings suggest that altered expression of A20 in HSPC contributes to an aging-like phenotype, and that there may be a common underlying mechanism for diminished HSPC function between inflammatory states and aging.
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Affiliation(s)
- Molly A Smith
- Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, United States
| | - Ashley E Culver-Cochran
- Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Emmalee R Adelman
- Department of Human Genetics, University of Miami, Miami, FL, United States
| | - Garrett W Rhyasen
- Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, United States
| | - Averil Ma
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Maria E Figueroa
- Department of Human Genetics, University of Miami, Miami, FL, United States.,Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States
| | - Daniel T Starczynowski
- Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, United States.,Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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Affiliation(s)
- Ashley E Culver-Cochran
- a Division of Experimental Hematology and Cancer Biology , Cincinnati Children's Hospital Medical Center , Cincinnati , OH , USA
| | - Daniel T Starczynowski
- a Division of Experimental Hematology and Cancer Biology , Cincinnati Children's Hospital Medical Center , Cincinnati , OH , USA.,b Department of Cancer Biology , University of Cincinnati , Cincinnati , OH , USA
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Zhang P, Culver-Cochran AE, Stevens SM, Liu B. Characterization of a SILAC method for proteomic analysis of primary rat microglia. Proteomics 2016; 16:1341-6. [PMID: 26936193 DOI: 10.1002/pmic.201500390] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/29/2016] [Accepted: 02/19/2016] [Indexed: 11/08/2022]
Abstract
Microglia play important and dynamic roles in mediating a variety of physiological and pathological processes during the development, normal function and degeneration of the central nervous system. Application of SILAC-based proteomic analysis would greatly facilitate the identification of cellular pathways regulating the multifaceted phenotypes of microglia. We and others have successfully SILAC-labeled immortalized murine microglial cell lines in previous studies. In this study, we report the development and evaluation of a SILAC-labeled primary rat microglia model. Although the isotope labeling scheme for primary microglia is drastically different from that of immortalized cell lines, our de novo and uninterrupted primary culture labeling protocol (DUP-SILAC) resulted in sufficient incorporation of SILAC labels for mass spectrometry-based proteomic profiling. In addition, label incorporation did not alter their morphology and response to endotoxin stimulation. Proteomic analysis of the endotoxin-stimulated SILAC-labeled primary microglia identified expected as well as potentially novel activation markers and pro-inflammatory pathways that could be quantified in a more physiologically relevant cellular model system compared to immortalized cell lines. The establishment of primary microglia SILAC model will further expand our capacity for global scale proteomic profiling of pathways under various physiological and pathological conditions. Proteomic MS data are available via ProteomeXchange with identifier PXD002759.
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Affiliation(s)
- Ping Zhang
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Ashley E Culver-Cochran
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Stanley M Stevens
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Bin Liu
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
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Bell-Temin H, Culver-Cochran AE, Chaput D, Carlson CM, Kuehl M, Burkhardt BR, Bickford PC, Liu B, Stevens SM. Novel Molecular Insights into Classical and Alternative Activation States of Microglia as Revealed by Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-based Proteomics. Mol Cell Proteomics 2015; 14:3173-84. [PMID: 26424600 PMCID: PMC4762627 DOI: 10.1074/mcp.m115.053926] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 11/21/2022] Open
Abstract
Microglia, the resident immune cells of the brain, have been shown to display a complex spectrum of roles that span from neurotrophic to neurotoxic depending on their activation status. Microglia can be classified into four stages of activation, M1, which most closely matches the classical (pro-inflammatory) activation stage, and the alternative activation stages M2a, M2b, and M2c. The alternative activation stages have not yet been comprehensively analyzed through unbiased, global-scale protein expression profiling. In this study, BV2 mouse immortalized microglial cells were stimulated with agonists specific for each of the four stages and total protein expression for 4644 protein groups was quantified using SILAC-based proteomic analysis. After validating induction of the various stages through a targeted cytokine assay and Western blotting of activation states, the data revealed novel insights into the similarities and differences between the various states. The data identify several protein groups whose expression in the anti-inflammatory, pro-healing activation states are altered presumably to curtail inflammatory activation through differential protein expression, in the M2a state including CD74, LYN, SQST1, TLR2, and CD14. The differential expression of these proteins promotes healing, limits phagocytosis, and limits activation of reactive nitrogen species through toll-like receptor cascades. The M2c state appears to center around the down-regulation of a key member in the formation of actin-rich phagosomes, SLP-76. In addition, the proteomic data identified a novel activation marker, DAB2, which is involved in clathrin-mediated endocytosis and is significantly different between M2a and either M1 or M2b states. Western blot analysis of mouse primary microglia stimulated with the various agonists of the classical and alternative activation states revealed a similar trend of DAB2 expression compared with BV2 cells.
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Affiliation(s)
- Harris Bell-Temin
- From the ‡Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620
| | - Ashley E Culver-Cochran
- From the ‡Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620
| | - Dale Chaput
- From the ‡Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620
| | - Christina M Carlson
- From the ‡Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620
| | - Melanie Kuehl
- From the ‡Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620
| | - Brant R Burkhardt
- From the ‡Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620
| | - Paula C Bickford
- §James A. Haley VA Hospital, Research Service and Department of Neurosurgery and Brain Repair, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, Florida 33612
| | - Bin Liu
- ¶Department of Pharmacodynamics, University of Florida, 1345 Center Drive, Gainesville, Florida 32610
| | - Stanley M Stevens
- From the ‡Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620;
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Culver-Cochran AE, Chadwick BP. Loss of WSTF results in spontaneous fluctuations of heterochromatin formation and resolution, combined with substantial changes to gene expression. BMC Genomics 2013; 14:740. [PMID: 24168170 PMCID: PMC3870985 DOI: 10.1186/1471-2164-14-740] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/26/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the maintenance of heterochromatin, including at the human inactive X chromosome (Xi). WSTF is encoded by BAZ1B, and is one of twenty-eight genes that are hemizygously deleted in the genetic disorder Williams-Beuren syndrome (WBS). RESULTS To explore the function of WSTF, we performed zinc finger nuclease-assisted targeting of the BAZ1B gene and isolated several independent knockout clones in human cells. Our results show that, while heterochromatin at the Xi is unaltered, new inappropriate areas of heterochromatin spontaneously form and resolve throughout the nucleus, appearing as large DAPI-dense staining blocks, defined by histone H3 lysine-9 trimethylation and association of the proteins heterochromatin protein 1 and structural maintenance of chromosomes flexible hinge domain containing 1. In three independent mutants, the expression of a large number of genes were impacted, both up and down, by WSTF loss. CONCLUSIONS Given the inappropriate appearance of regions of heterochromatin in BAZ1B knockout cells, it is evident that WSTF performs a critical role in maintaining chromatin and transcriptional states, a property that is likely compromised by WSTF haploinsufficiency in WBS patients.
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Affiliation(s)
| | - Brian P Chadwick
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
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