1
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Espejo-Serrano C, Aitken C, Tan BF, May DG, Chrisopulos RJ, Roux KJ, Demmers JA, Mackintosh SG, Gribnau J, Bustos F, Gontan C, Findlay GM. Chromatin targeting of the RNF12/RLIM E3 ubiquitin ligase controls transcriptional responses. Life Sci Alliance 2024; 7:e202302282. [PMID: 38199845 PMCID: PMC10781586 DOI: 10.26508/lsa.202302282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Protein ubiquitylation regulates key biological processes including transcription. This is exemplified by the E3 ubiquitin ligase RNF12/RLIM, which controls developmental gene expression by ubiquitylating the REX1 transcription factor and is mutated in an X-linked intellectual disability disorder. However, the precise mechanisms by which ubiquitylation drives specific transcriptional responses are not known. Here, we show that RNF12 is recruited to specific genomic locations via a consensus sequence motif, which enables co-localisation with REX1 substrate at gene promoters. Surprisingly, RNF12 chromatin recruitment is achieved via a non-catalytic basic region and comprises a previously unappreciated N-terminal autoinhibitory mechanism. Furthermore, RNF12 chromatin targeting is critical for REX1 ubiquitylation and downstream RNF12-dependent gene regulation. Our results demonstrate a key role for chromatin in regulation of the RNF12-REX1 axis and provide insight into mechanisms by which protein ubiquitylation enables programming of gene expression.
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Affiliation(s)
- Carmen Espejo-Serrano
- https://ror.org/01zg1tt02 MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Catriona Aitken
- https://ror.org/01zg1tt02 MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Beatrice F Tan
- https://ror.org/018906e22 Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Danielle G May
- https://ror.org/00sfn8y78 Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
| | - Rachel J Chrisopulos
- https://ror.org/00sfn8y78 Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
| | - Kyle J Roux
- https://ror.org/00sfn8y78 Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
| | - Jeroen Aa Demmers
- https://ror.org/018906e22 Proteomics Center and Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Joost Gribnau
- https://ror.org/018906e22 Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Francisco Bustos
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
- https://ror.org/00sfn8y78 Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
| | - Cristina Gontan
- https://ror.org/018906e22 Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Greg M Findlay
- https://ror.org/01zg1tt02 MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
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2
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Garg S, Morehead LC, Bird JT, Graw S, Gies A, Storey AJ, Tackett AJ, Edmondson RD, Mackintosh SG, Byrum SD, Miousse IR. Characterization of methionine dependence in melanoma cells. Mol Omics 2024; 20:37-47. [PMID: 37782107 PMCID: PMC10903584 DOI: 10.1039/d3mo00087g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Dietary methionine restriction is associated with a reduction in tumor growth in preclinical studies and an increase in lifespan in animal models. The mechanism by which methionine restriction inhibits tumor growth while sparing normal cells is incompletely understood. We do know that normal cells can utilize methionine or homocysteine interchangeably (methionine independence) while most cancer cells are strictly dependent on methionine availability. Here, we compared a typical methionine dependent and a rare methionine independent melanoma cell line. We show that replacing methionine, a methyl donor, with its precursor homocysteine generally induced hypomethylation in gene promoters. This decrease was similar in methionine dependent and methionine independent cells. There was only a low level of pathway enrichment, suggesting that the hypomethylation is generalized rather than gene specific. Whole proteome and transcriptome were also analyzed. This analysis revealed that contrarily to the effect on methylation, the replacement of methionine with homocysteine had a much greater effect on the transcriptome and proteome of methionine dependent cells than methionine independent cells. Interestingly, methionine adenosyltransferase 2A (MAT2A), responsible for the synthesis of S-adenosylmethionine from methionine, was equally strongly upregulated in both cell lines. This suggests that the absence of methionine is equally detected but triggers different outcomes in methionine dependent versus independent cells. Our analysis reveals the importance of cell cycle control, DNA damage repair, translation, nutrient sensing, oxidative stress and immune functions in the cellular response to methionine stress in melanoma.
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Affiliation(s)
- Sarita Garg
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - Lauren C Morehead
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - Jordan T Bird
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - Stefan Graw
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - Allen Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - Rick D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - Isabelle R Miousse
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
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3
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Zhao S, Lu J, Pan B, Fan H, Byrum SD, Xu C, Kim A, Guo Y, Kanchi KL, Gong W, Sun T, Storey AJ, Burkholder NT, Mackintosh SG, Kuhlers PC, Edmondson RD, Strahl BD, Diao Y, Tackett AJ, Raab JR, Cai L, Song J, Wang GG. TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons. Nature 2023; 623:633-642. [PMID: 37938770 PMCID: PMC11000523 DOI: 10.1038/s41586-023-06688-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/27/2023] [Indexed: 11/09/2023]
Abstract
Trimethylation of histone H3 lysine 9 (H3K9me3) is crucial for the regulation of gene repression and heterochromatin formation, cell-fate determination and organismal development1. H3K9me3 also provides an essential mechanism for silencing transposable elements1-4. However, previous studies have shown that canonical H3K9me3 readers (for example, HP1 (refs. 5-9) and MPP8 (refs. 10-12)) have limited roles in silencing endogenous retroviruses (ERVs), one of the main transposable element classes in the mammalian genome13. Here we report that trinucleotide-repeat-containing 18 (TNRC18), a poorly understood chromatin regulator, recognizes H3K9me3 to mediate the silencing of ERV class I (ERV1) elements such as LTR12 (ref. 14). Biochemical, biophysical and structural studies identified the carboxy-terminal bromo-adjacent homology (BAH) domain of TNRC18 (TNRC18(BAH)) as an H3K9me3-specific reader. Moreover, the amino-terminal segment of TNRC18 is a platform for the direct recruitment of co-repressors such as HDAC-Sin3-NCoR complexes, thus enforcing optimal repression of the H3K9me3-demarcated ERVs. Point mutagenesis that disrupts the TNRC18(BAH)-mediated H3K9me3 engagement caused neonatal death in mice and, in multiple mammalian cell models, led to derepressed expression of ERVs, which affected the landscape of cis-regulatory elements and, therefore, gene-expression programmes. Collectively, we describe a new H3K9me3-sensing and regulatory pathway that operates to epigenetically silence evolutionarily young ERVs and exert substantial effects on host genome integrity, transcriptomic regulation, immunity and development.
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Affiliation(s)
- Shuai Zhao
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Bo Pan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
| | - Huitao Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Chenxi Xu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Arum Kim
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Yiran Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Krishna L Kanchi
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Tongyu Sun
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Nathaniel T Burkholder
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Peyton C Kuhlers
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian D Strahl
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Yarui Diao
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jesse R Raab
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Ling Cai
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, USA.
| | - Gang Greg Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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4
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Hashimi M, Sebrell TA, Hedges JF, Snyder D, Lyon KN, Byrum SD, Mackintosh SG, Crowley D, Cherne MD, Skwarchuk D, Robison A, Sidar B, Kunze A, Loveday EK, Taylor MP, Chang CB, Wilking JN, Walk ST, Schountz T, Jutila MA, Bimczok D. Antiviral responses in a Jamaican fruit bat intestinal organoid model of SARS-CoV-2 infection. Nat Commun 2023; 14:6882. [PMID: 37898615 PMCID: PMC10613288 DOI: 10.1038/s41467-023-42610-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Bats are natural reservoirs for several zoonotic viruses, potentially due to an enhanced capacity to control viral infection. However, the mechanisms of antiviral responses in bats are poorly defined. Here we established a Jamaican fruit bat (JFB, Artibeus jamaicensis) intestinal organoid model of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Upon infection with SARS-CoV-2, increased viral RNA and subgenomic RNA was detected, but no infectious virus was released, indicating that JFB organoids support only limited viral replication but not viral reproduction. SARS-CoV-2 replication was associated with significantly increased gene expression of type I interferons and inflammatory cytokines. Interestingly, SARS-CoV-2 also caused enhanced formation and growth of JFB organoids. Proteomics revealed an increase in inflammatory signaling, cell turnover, cell repair, and SARS-CoV-2 infection pathways. Collectively, our findings suggest that primary JFB intestinal epithelial cells mount successful antiviral interferon responses and that SARS-CoV-2 infection in JFB cells induces protective regenerative pathways.
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Affiliation(s)
- Marziah Hashimi
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - T Andrew Sebrell
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Jodi F Hedges
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Deann Snyder
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Katrina N Lyon
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Stephanie D Byrum
- University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, Little Rock, AR, USA
- Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Samuel G Mackintosh
- University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, Little Rock, AR, USA
| | - Dan Crowley
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
- Department of Public & Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Michelle D Cherne
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - David Skwarchuk
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Amanda Robison
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Barkan Sidar
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
| | - Anja Kunze
- Montana State University, Electrical and Computer Engineering Department, Bozeman, MT, USA
| | - Emma K Loveday
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
| | - Matthew P Taylor
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Connie B Chang
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - James N Wilking
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Seth T Walk
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology and Center of Vector-Borne Infectious Diseases, Colorado State University, Fort, Collins, CO, USA
| | - Mark A Jutila
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Diane Bimczok
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA.
- Center for Biofilm Engineering, Bozeman, MT, USA.
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5
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Seman A, Chandra PK, Byrum SD, Mackintosh SG, Gies AJ, Busija DW, Rutkai I. Targeting mitochondria in the aged cerebral vasculature with SS-31, a proteomic study of brain microvessels. GeroScience 2023; 45:2951-2965. [PMID: 37458933 PMCID: PMC10643806 DOI: 10.1007/s11357-023-00845-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/28/2023] [Indexed: 08/20/2023] Open
Abstract
Cognitive impairment and dementias during aging such as Alzheimer's disease are linked to functional decline and structural alterations of the brain microvasculature. Although mechanisms leading to microvascular changes during aging are not clear, loss of mitochondria, and reduced efficiency of remaining mitochondria appear to play a major role. Pharmacological agents, such as SS-31, which target mitochondria have been shown to be effective during aging and diseases; however, the benefit to mitochondrial- and non-mitochondrial proteins in the brain microvasculature has not been examined. We tested whether attenuation of aging-associated changes in the brain microvascular proteome via targeting mitochondria represents a therapeutic option for the aging brain. We used aged male (> 18 months) C57Bl6/J mice treated with a mitochondria-targeted tetrapeptide, SS-31, or vehicle saline. Cerebral blood flow (CBF) was determined using laser speckle imaging during a 2-week treatment period. Then, isolated cortical microvessels (MVs) composed of end arterioles, capillaries, and venules were used for Orbitrap Eclipse Tribrid mass spectrometry. CBF was similar among the groups, whereas bioinformatic analysis revealed substantial differences in protein abundance of cortical MVs between SS-31 and vehicle. We identified 6267 proteins, of which 12% were mitochondria-associated. Of this 12%, 107 were significantly differentially expressed and were associated with oxidative phosphorylation, metabolism, the antioxidant defense system, or mitochondrial dynamics. Administration of SS-31 affected many non-mitochondrial proteins. Our findings suggest that mitochondria in the microvasculature represent a therapeutic target in the aging brain, and widespread changes in the proteome may underlie the rejuvenating actions of SS-31 in aging.
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Affiliation(s)
- Abigail Seman
- Department of Pharmacology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Partha K Chandra
- Department of Pharmacology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
- Tulane Brain Institute, Tulane University, 200 Flower Hall, New Orleans, LA, 70118, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA
| | - Allen J Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA
| | - David W Busija
- Department of Pharmacology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
- Tulane Brain Institute, Tulane University, 200 Flower Hall, New Orleans, LA, 70118, USA
| | - Ibolya Rutkai
- Department of Pharmacology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA.
- Tulane Brain Institute, Tulane University, 200 Flower Hall, New Orleans, LA, 70118, USA.
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6
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Todorova VK, Byrum SD, Mackintosh SG, Jamshidi-Parsian A, Gies AJ, Washam CL, Jenkins SV, Spiva T, Bowman E, Reyna NS, Griffin RJ, Makhoul I. Exosomal MicroRNA and Protein Profiles of Hepatitis B Virus-Related Hepatocellular Carcinoma Cells. Int J Mol Sci 2023; 24:13098. [PMID: 37685904 PMCID: PMC10487651 DOI: 10.3390/ijms241713098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Infection with hepatitis B virus (HBV) is a main risk factor for hepatocellular carcinoma (HCC). Extracellular vesicles, such as exosomes, play an important role in tumor development and metastasis, including regulation of HBV-related HCC. In this study, we have characterized exosome microRNA and proteins released in vitro from hepatitis B virus (HBV)-related HCC cell lines SNU-423 and SNU-182 and immortalized normal hepatocyte cell lines (THLE2 and THLE3) using microRNA sequencing and mass spectrometry. Bioinformatics, including functional enrichment and network analysis, combined with survival analysis using data related to HCC in The Cancer Genome Atlas (TCGA) database, were applied to examine the prognostic significance of the results. More than 40 microRNAs and 200 proteins were significantly dysregulated (p < 0.05) in the exosomes released from HCC cells in comparison with the normal liver cells. The functional analysis of the differentially expressed exosomal miRNAs (i.e., mir-483, mir-133a, mir-34a, mir-155, mir-183, mir-182), their predicted targets, and exosomal differentially expressed proteins (i.e., POSTN, STAM, EXOC8, SNX9, COL1A2, IDH1, FN1) showed correlation with pathways associated with HBV, virus activity and invasion, exosome formation and adhesion, and exogenous protein binding. The results from this study may help in our understanding of the role of HBV infection in the development of HCC and in the development of new targets for treatment or non-invasive predictive biomarkers of HCC.
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Affiliation(s)
- Valentina K. Todorova
- Department of Internal Medicine/Division of Hematology/Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Stephanie D. Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Azemat Jamshidi-Parsian
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (A.J.-P.); (S.V.J.); (R.J.G.)
| | - Allen J. Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Charity L. Washam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Samir V. Jenkins
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (A.J.-P.); (S.V.J.); (R.J.G.)
| | - Timothy Spiva
- Biology Department, Ouachita Baptist University, Arkadelphia, AR 71998, USA; (T.S.); (E.B.); (N.S.R.)
| | - Emily Bowman
- Biology Department, Ouachita Baptist University, Arkadelphia, AR 71998, USA; (T.S.); (E.B.); (N.S.R.)
| | - Nathan S. Reyna
- Biology Department, Ouachita Baptist University, Arkadelphia, AR 71998, USA; (T.S.); (E.B.); (N.S.R.)
| | - Robert J. Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (A.J.-P.); (S.V.J.); (R.J.G.)
| | - Issam Makhoul
- Department of Internal Medicine/Division of Hematology/Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
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7
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Chen M, Li J, Zhang L, Wang L, Cheng C, Ji H, Altilia S, Ding X, Cai G, Altomare D, Shtutman M, Byrum SD, Mackintosh SG, Feoktistov A, Soshnikova N, Mogila VA, Tatarskiy V, Erokhin M, Chetverina D, Prawira A, Ni Y, Urban S, McInnes C, Broude EV, Roninson IB. CDK8 and CDK19: positive regulators of signal-induced transcription and negative regulators of Mediator complex proteins. Nucleic Acids Res 2023; 51:7288-7313. [PMID: 37378433 PMCID: PMC10415139 DOI: 10.1093/nar/gkad538] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
We have conducted a detailed transcriptomic, proteomic and phosphoproteomic analysis of CDK8 and its paralog CDK19, alternative enzymatic components of the kinase module associated with transcriptional Mediator complex and implicated in development and diseases. This analysis was performed using genetic modifications of CDK8 and CDK19, selective CDK8/19 small molecule kinase inhibitors and a potent CDK8/19 PROTAC degrader. CDK8/19 inhibition in cells exposed to serum or to agonists of NFκB or protein kinase C (PKC) reduced the induction of signal-responsive genes, indicating a pleiotropic role of Mediator kinases in signal-induced transcriptional reprogramming. CDK8/19 inhibition under basal conditions initially downregulated a small group of genes, most of which were inducible by serum or PKC stimulation. Prolonged CDK8/19 inhibition or mutagenesis upregulated a larger gene set, along with a post-transcriptional increase in the proteins comprising the core Mediator complex and its kinase module. Regulation of both RNA and protein expression required CDK8/19 kinase activities but both enzymes protected their binding partner cyclin C from proteolytic degradation in a kinase-independent manner. Analysis of isogenic cell populations expressing CDK8, CDK19 or their kinase-inactive mutants revealed that CDK8 and CDK19 have the same qualitative effects on protein phosphorylation and gene expression at the RNA and protein levels, whereas differential effects of CDK8 versus CDK19 knockouts were attributable to quantitative differences in their expression and activity rather than different functions.
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Affiliation(s)
- Mengqian Chen
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
- Senex Biotechnology, Inc. Columbia, SC 29208, USA
| | - Jing Li
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Li Zhang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Lili Wang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Chen Cheng
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Hao Ji
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Serena Altilia
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaokai Ding
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Guoshuai Cai
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Diego Altomare
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Michael Shtutman
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alexey Feoktistov
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Nataliya Soshnikova
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Vladislav A Mogila
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Victor Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Angga Prawira
- Department of Infectious Diseases, University Hospital of Heidelberg, Heidelberg, Germany
| | - Yi Ni
- Department of Infectious Diseases, University Hospital of Heidelberg, Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, University Hospital of Heidelberg, Heidelberg, Germany
| | - Campbell McInnes
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Eugenia V Broude
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Igor B Roninson
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
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8
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Garg S, Morehead LC, Bird JT, Graw S, Gies A, Storey AJ, Tackett AJ, Edmondson RD, Mackintosh SG, Byrum SD, Miousse IR. Characterization of methionine dependence in melanoma cells. bioRxiv 2023:2023.04.05.535723. [PMID: 37066392 PMCID: PMC10104025 DOI: 10.1101/2023.04.05.535723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Dietary methionine restriction is associated with a reduction in tumor growth in preclinical studies and an increase in lifespan in animal models. The mechanism by which methionine restriction inhibits tumor growth while sparing normal cells is incompletely understood. We do know that normal cells can utilize methionine or homocysteine interchangeably (methionine independence) while most cancer cells are strictly dependent on methionine availability. Here, we compared a typical methionine dependent and a rare methionine independent melanoma cell line. We show that replacing methionine, a methyl donor, with its precursor homocysteine generally induced hypomethylation in gene promoters. This decrease was similar in methionine dependent and methionine independent cells. There was only a low level of pathway enrichment, suggesting that the hypomethylation is generalized rather than gene specific. Whole proteome and transcriptome were also analyzed. This analysis revealed that contrarily to the effect on methylation, the replacement of methionine with homocysteine had a much greater effect on the transcriptome and proteome of methionine dependent cells than methionine independent cells. Interestingly, methionine adenosyltransferase 2A (MAT2A), responsible for the synthesis of s-adenosylmethionine from methionine, was equally strongly upregulated in both cell lines. This suggests that the absence of methionine is equally detected but triggers different outcomes in methionine dependent versus independent cells. Our analysis reveals the importance of cell cycle control, DNA damage repair, translation, nutrient sensing, oxidative stress and immune functions in the cellular response to methionine stress in melanoma.
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Affiliation(s)
- Sarita Garg
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Lauren C Morehead
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Jordan T Bird
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Stefan Graw
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Allen Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Rick D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Isabelle R Miousse
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
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9
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Pei J, Xiao Y, Liu X, Hu W, Sobh A, Yuan Y, Zhou S, Hua N, Mackintosh SG, Zhang X, Basso KB, Kamat M, Yang Q, Licht JD, Zheng G, Zhou D, Lv D. Piperlongumine conjugates induce targeted protein degradation. Cell Chem Biol 2023; 30:203-213.e17. [PMID: 36750097 PMCID: PMC10074544 DOI: 10.1016/j.chembiol.2023.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/31/2022] [Accepted: 01/17/2023] [Indexed: 02/09/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that degrade target proteins through recruiting E3 ligases. However, their application is limited in part because few E3 ligases can be recruited by known E3 ligase ligands. In this study, we identified piperlongumine (PL), a natural product, as a covalent E3 ligase recruiter, which induces CDK9 degradation when it is conjugated with SNS-032, a CDK9 inhibitor. The lead conjugate 955 can potently degrade CDK9 in a ubiquitin-proteasome-dependent manner and is much more potent than SNS-032 against various tumor cells in vitro. Mechanistically, we identified KEAP1 as the E3 ligase recruited by 955 to degrade CDK9 through a TurboID-based proteomics study, which was further confirmed by KEAP1 knockout and the nanoBRET ternary complex formation assay. In addition, PL-ceritinib conjugate can degrade EML4-ALK fusion oncoprotein, suggesting that PL may have a broader application as a covalent E3 ligase ligand in targeted protein degradation.
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Affiliation(s)
- Jing Pei
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Xingui Liu
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Wanyi Hu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Amin Sobh
- Division of Hematology/Oncology, University of Florida Health Cancer Center, 2033 Mowry Road, Suite 145, Gainesville, FL 32610, USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Shuo Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Nan Hua
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 803, Little Rock, AR 72205, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Kari B Basso
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Manasi Kamat
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Qingping Yang
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida Health Cancer Center, 2033 Mowry Road, Suite 145, Gainesville, FL 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA.
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA; Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Dongwen Lv
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA; Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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10
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Hashimi M, Sebrell T, Hedges J, Snyder D, Lyon K, Byrum S, Mackintosh SG, Cherne M, Skwarchuk D, Crowley D, Robison A, Sidar B, Kunze A, Loveday E, Taylor M, Chang C, Wilking J, Walk S, Schountz T, Jutila M, Bimczok D. Antiviral response mechanisms in a Jamaican Fruit Bat intestinal organoid model of SARS-CoV-2 infection. Res Sq 2022:rs.3.rs-2340919. [PMID: 36561186 PMCID: PMC9774215 DOI: 10.21203/rs.3.rs-2340919/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bats are natural reservoirs for several zoonotic viruses, potentially due to an enhanced capacity to control viral infection. However, the mechanisms of antiviral responses in bats are poorly defined. Here we established a Jamaican fruit bat (JFB) intestinal organoid model of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. JFB organoids were susceptible to SARS-CoV-2 infection, with increased viral RNA and subgenomic RNA detected in cell lysates and supernatants. Gene expression of type I interferons and inflammatory cytokines was induced in response to SARS-CoV-2 but not in response to TLR agonists. Interestingly, SARS-CoV-2 did not lead to cytopathic effects in JFB organoids but caused enhanced organoid growth. Proteomic analyses revealed an increase in inflammatory signaling, cell turnover, cell repair, and SARS-CoV-2 infection pathways. Collectively, our findings suggest that primary JFB intestinal epithelial cells can mount a successful antiviral interferon response and that SARS-CoV-2 infection in JFB cells induces protective regenerative pathways.
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11
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Chau MJ, Quintero JE, Blalock E, Byrum S, Mackintosh SG, Samaan C, Gerhardt GA, van Horne CG. Transection injury differentially alters the proteome of the human sural nerve. PLoS One 2022; 17:e0260998. [PMID: 36417411 PMCID: PMC9683555 DOI: 10.1371/journal.pone.0260998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 09/09/2022] [Indexed: 11/25/2022] Open
Abstract
Regeneration after severe peripheral nerve injury is often poor. Knowledge of human nerve regeneration and the growth microenvironment is greatly lacking. We aimed to identify the regenerative proteins in human peripheral nerve by comparing the proteome before and after a transection injury. In a unique study design, we collected closely matched samples of naïve and injured sural nerve. Naïve and injured (two weeks after injury) samples were analyzed using mass spectrometry and immunoassays. We found significantly altered levels following the nerve injury. Mass spectrometry revealed that injury samples had 568 proteins significantly upregulated and 471 significantly downregulated compared to naïve samples (q-value ≤ 0.05 and Z ≥ |2| (log2)). We used Gene Ontology (GO) pathway overrepresentation analysis to highlight groups of proteins that were significantly upregulated or downregulated with injury-induced degeneration and regeneration. Significant protein changes in key pathways were identified including growth factor levels, Schwann cell de-differentiation, myelination downregulation, epithelial-mesenchymal transition (EMT), and axonal regeneration pathways. The proteomes of the uninjured nerve compared to the degenerating/regenerating nerve may reveal biomarkers to aid in the development of repair strategies such as infusing supplemental trophic factors and in monitoring neural tissue regeneration.
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Affiliation(s)
- Monica J. Chau
- Brain Restoration Center, College of Medicine, University of Kentucky, Lexington, KY, United States of America
- Department of Neurosurgery, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Jorge E. Quintero
- Brain Restoration Center, College of Medicine, University of Kentucky, Lexington, KY, United States of America
- Department of Neurosurgery, College of Medicine, University of Kentucky, Lexington, KY, United States of America
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Eric Blalock
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Stephanie Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Christopher Samaan
- Brain Restoration Center, College of Medicine, University of Kentucky, Lexington, KY, United States of America
- Department of Neurosurgery, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Greg A. Gerhardt
- Brain Restoration Center, College of Medicine, University of Kentucky, Lexington, KY, United States of America
- Department of Neurosurgery, College of Medicine, University of Kentucky, Lexington, KY, United States of America
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, United States of America
- Department of Neurology, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Craig G. van Horne
- Brain Restoration Center, College of Medicine, University of Kentucky, Lexington, KY, United States of America
- Department of Neurosurgery, College of Medicine, University of Kentucky, Lexington, KY, United States of America
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, United States of America
- * E-mail:
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12
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Scieszka D, Byrum SD, Mackintosh SG, Madison M, Knight J, Campen MJ, Kheradmand F. Subchronic Electronic Cigarette Exposures Have Overlapping Protein Biomarkers with Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2022; 67:503-506. [PMID: 36178855 PMCID: PMC9564931 DOI: 10.1165/rcmb.2021-0482le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
| | - Stephanie D. Byrum
- University of Arkansas Medical SciencesLittle Rock, Arkansas
- Arkansas Children’s Research InstituteLittle Rock, Arkansas
| | | | | | | | | | - Farrah Kheradmand
- Baylor College of MedicineHouston, Texas
- Michael E. DeBakey Veterans Affairs Medical CenterHouston, Texas
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13
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Das BK, Wang L, Fujiwara T, Zhou J, Aykin-Burns N, Krager KJ, Lan R, Mackintosh SG, Edmondson R, Jennings ML, Wang X, Feng JQ, Barrientos T, Gogoi J, Kannan A, Gao L, Xing W, Mohan S, Zhao H. Transferrin receptor 1-mediated iron uptake regulates bone mass in mice via osteoclast mitochondria and cytoskeleton. eLife 2022; 11:73539. [PMID: 35758636 PMCID: PMC9352353 DOI: 10.7554/elife.73539] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 06/25/2022] [Indexed: 11/13/2022] Open
Abstract
Increased intracellular iron spurs mitochondrial biogenesis and respiration to satisfy high-energy demand during osteoclast differentiation and bone-resorbing activities. Transferrin receptor 1 (Tfr1) mediates cellular iron uptake through endocytosis of iron-loaded transferrin, and its expression increases during osteoclast differentiation. Nonetheless, the precise functions of Tfr1 and Tfr1-mediated iron uptake in osteoclast biology and skeletal homeostasis remain incompletely understood. To investigate the role of Tfr1 in osteoclast lineage cells in vivo and in vitro, we crossed Tfrc (encoding Tfr1)-floxed mice with Lyz2 (LysM)-Cre and Cathepsin K (Ctsk)-Cre mice to generate Tfrc conditional knockout mice in myeloid osteoclast precursors (Tfr1ΔLysM) or differentiated osteoclasts (Tfr1ΔCtsk), respectively. Skeletal phenotyping by µCT and histology unveiled a significant increase in trabecular bone mass with normal osteoclast number in long bones of 10-week-old young and 6-month-old adult female but not male Tfr1ΔLysM mice. Although high trabecular bone volume in long bones was observed in both male and female Tfr1ΔCtsk mice, this phenotype was more pronounced in female knockout mice. Consistent with this gender-dependent phenomena, estrogen deficiency induced by ovariectomy decreased trabecular bone mass in Tfr1ΔLysM mice. Mechanistically, disruption of Tfr1 expression attenuated mitochondrial metabolism and cytoskeletal organization in mature osteoclasts in vitro by attenuating mitochondrial respiration and activation of the Src-Rac1-WAVE regulatory complex axis, respectively, leading to decreased bone resorption with little impact on osteoclast differentiation. These results indicate that Tfr1-mediated iron uptake is specifically required for osteoclast function and is indispensable for bone remodeling in a gender-dependent manner.
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Affiliation(s)
- Bhaba K Das
- Long Beach VA Healthcare System, Southern California Institute for Research and Education, Long Beach, United States
| | - Lei Wang
- Department of Orthopedics, Anhui Medical University, Hefei, China
| | - Toshifumi Fujiwara
- Department of Orthopedic Surgery, Kyushu University Hospital, Fukuoka, Japan
| | - Jian Zhou
- Department of Orthopedics, Anhui Medical University, HeFei, China
| | - Nukhet Aykin-Burns
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, United States
| | - Kimberly J Krager
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, United States
| | - Renny Lan
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, United States
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, United States
| | - Ricky Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, United States
| | - Michael L Jennings
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, United States
| | - Xiaofang Wang
- Department of Biomedical Sciences, Texas A&M University, Dallas, United States
| | - Jian Q Feng
- Department of Biomedical Sciences, Texas A&M University, Dallas, United States
| | | | - Jyoti Gogoi
- Long Beach VA Healthcare System, Southern California Institute for Research and Education, Long Beach, United States
| | - Aarthi Kannan
- Long Beach VA Healthcare System, Southern California Institute for Research and Education, Long Beach, United States
| | - Ling Gao
- Long Beach VA Healthcare System, Southern California Institute for Research and Education, Long Beach, United States
| | - Weirong Xing
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, Loma Linda, United States
| | - Subburaman Mohan
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, Loma Linda, United States
| | - Haibo Zhao
- Long Beach VA Healthcare System, Southern California Institute for Research and Education, Long Beach, United States
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14
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Li D, Yu X, Kottur J, Gong W, Zhang Z, Storey AJ, Tsai YH, Uryu H, Shen Y, Byrum SD, Edmondson RD, Mackintosh SG, Cai L, Liu Z, Aggarwal AK, Tackett AJ, Liu J, Jin J, Wang GG. Discovery of a dual WDR5 and Ikaros PROTAC degrader as an anti-cancer therapeutic. Oncogene 2022; 41:3328-3340. [PMID: 35525905 PMCID: PMC9189076 DOI: 10.1038/s41388-022-02340-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/21/2022]
Abstract
WD repeat domain 5 (WDR5), an integral component of the MLL/KMT2A lysine methyltransferase complex, is critically involved in oncogenesis and represents an attractive onco-target. Inhibitors targeting protein-protein interactions (PPIs) between WDR5 and its binding partners, however, do not inhibit all of WDR5-mediated oncogenic functions and exert rather limited antitumor effects. Here, we report a cereblon (CRBN)-recruiting proteolysis targeting chimera (PROTAC) of WDR5, MS40, which selectively degrades WDR5 and the well-established neo-substrates of immunomodulatory drugs (IMiDs):CRBN, the Ikaros zinc finger (IKZF) transcription factors IKZF1 and IKZF3. MS40-induced WDR5 degradation caused disassociation of the MLL/KMT2A complex off chromatin, resulting in decreased H3K4me2. Transcriptomic profiling revealed that targets of both WDR5 and IMiDs:CRBN were significantly repressed by treatment of MS40. In MLL-rearranged leukemias, which exhibit IKZF1 high expression and dependency, co-suppression of WDR5 and Ikaros by MS40 is superior in suppressing oncogenesis to the WDR5 PPI inhibitor, to MS40's non-PROTAC analog controls (MS40N1 and MS40N2, which do not bind CRBN and WDR5, respectively), and to a matched VHL-based WDR5 PROTAC (MS169, which degrades WDR5 but not Ikaros). MS40 suppressed the growth of primary leukemia patient cells in vitro and patient-derived xenografts in vivo. Thus, dual degradation of WDR5 and Ikaros is a promising anti-cancer strategy.
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Affiliation(s)
- Dongxu Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jithesh Kottur
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhao Zhang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hidetaka Uryu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yudao Shen
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Rick D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Aneel K Aggarwal
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jing Liu
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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15
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Vazquez JH, Kennon-McGill S, Byrum SD, Mackintosh SG, Jaeschke H, Williams DK, Lee WM, Dranoff JA, McGill MR. Proteomics Indicates Lactate Dehydrogenase Is Prognostic in Acetaminophen-Induced Acute Liver Failure Patients and Reveals Altered Signaling Pathways. Toxicol Sci 2022; 187:25-34. [PMID: 35172013 PMCID: PMC9216044 DOI: 10.1093/toxsci/kfac015] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Better biomarkers to predict death early in acute liver failure (ALF) are needed. To that end, we obtained early (study day 1) and later (day 3) serum samples from transplant-free survivors (n = 28) and nonsurvivors (n = 30) of acetaminophen-induced ALF from the NIH-sponsored Acute Liver Failure Study Group and from control volunteers (n = 10). To identify proteins that increase early in serum during ALF, we selected individuals from this cohort for whom alanine aminotransferase was lower on day 1 than day 3, indicating a time point before peak injury (n = 10/group). We then performed untargeted proteomics on their day 1 samples. Out of 1682 quantifiable proteins, 361 were ≥ 4-fold elevated or decreased in ALF patients versus controls and 16 of those were further elevated or decreased ≥ 4-fold in nonsurvivors versus survivors, indicating potential to predict death. Interestingly, 1 of the biomarkers was lactate dehydrogenase (LDH), which is already measured in most clinical laboratories. To validate our proteomics results and to confirm the prognostic potential of LDH, we measured LDH activity in all day 1 and 3 samples from all 58 ALF patients. LDH was elevated in the nonsurvivors versus survivors on both days. In addition, it had prognostic value similar to the model for end-stage liver disease and outperformed the King's College Criteria, while a combination of model for end-stage liver disease and LDH together outperformed either alone. Finally, bioinformatics analysis of our proteomics data revealed alteration of numerous signaling pathways that may be important in liver regeneration. Overall, we conclude LDH can predict death in APAP-induced ALF.
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Affiliation(s)
- Joel H Vazquez
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Stefanie Kennon-McGill
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Hartmut Jaeschke
- Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - D Keith Williams
- Department of Biostatistics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - William M Lee
- Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Med School, Dallas, Texas 75390, USA
| | - Jonathan A Dranoff
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Mitchell R McGill
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
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16
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Xu C, Meng F, Park KS, Storey AJ, Gong W, Tsai YH, Gibson E, Byrum SD, Li D, Edmondson RD, Mackintosh SG, Vedadi M, Cai L, Tackett AJ, Kaniskan HÜ, Jin J, Wang GG. A NSD3-targeted PROTAC suppresses NSD3 and cMyc oncogenic nodes in cancer cells. Cell Chem Biol 2022; 29:386-397.e9. [PMID: 34469831 PMCID: PMC8882712 DOI: 10.1016/j.chembiol.2021.08.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/14/2021] [Accepted: 08/12/2021] [Indexed: 12/26/2022]
Abstract
Nuclear receptor binding SET domain protein 3 (NSD3), a gene located within the 8p11-p12 amplicon frequently detected in human cancers, encodes a chromatin modulator and an attractive onco-target. However, agents that effectively suppress NSD3-mediated oncogenic actions are currently lacking. We report the NSD3-targeting proteolysis targeting chimera (PROTAC), MS9715, which achieves effective and specific targeting of NSD3 and associated cMyc node in tumor cells. MS9715 is designed by linking BI-9321, a NSD3 antagonist, which binds NSD3's PWWP1 domain, with an E3 ligase VHL ligand. Importantly, MS9715, but not BI-9321, effectively suppresses growth of NSD3-dependent hematological cancer cells. Transcriptomic profiling demonstrates that MS9715, but not BI-9321, effectively suppresses NSD3-and cMyc-associated gene expression programs, resembling effects of the CRISPR-Cas9-mediated knockout of NSD3. Collectively, these results suggest that pharmacological degradation of NSD3 as an attractive therapeutic strategy, which co-suppresses NSD3- and cMyc-related oncogenic nodes, is superior to blocking the PWWP1 domain of NSD3.
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Affiliation(s)
- Chenxi Xu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Fanye Meng
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kwang-Su Park
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Elisa Gibson
- Structural Genomics Consortium, University of Toronto, Toronto ON M5G 1L7, Canada
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Dongxu Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Rick D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto ON M5S 1A8, Canada
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
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17
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Waldrip ZJ, Burdine L, Harrison DK, Azevedo-Pouly AC, Storey AJ, Moffett OG, Mackintosh SG, Burdine MS. DNA-PKcs kinase activity stabilizes the transcription factor Egr1 in activated immune cells. J Biol Chem 2021; 297:101209. [PMID: 34562454 PMCID: PMC8551498 DOI: 10.1016/j.jbc.2021.101209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is known primarily for its function in DNA double-stranded break repair and nonhomologous end joining (NHEJ). However, DNA-PKcs also has a critical yet undefined role in immunity impacting both myeloid and lymphoid cell lineages spurring interest in targeting DNA-PKcs for therapeutic strategies in immune-related diseases. To gain insight into the function of DNA-PKcs within immune cells, we performed a quantitative phosphoproteomic screen in T cells to identify phosphorylation targets of DNA-PKcs. Our results indicate that DNA-PKcs phosphorylates the transcription factor Egr1 (early growth response protein 1) at serine 301. Expression of Egr1 is induced early upon T cell activation and dictates T cell response by modulating expression of cytokines and key costimulatory molecules such as IL (interleukin) 2, IL6, IFNγ, and NFκB. Inhibition of DNA-PKcs by treatment with a DNA-PKcs specific inhibitor NU7441 or shRNA knockdown increased proteasomal degradation of Egr1. Mutation of serine 301 to alanine via CRISPR-Cas9 reduced EGR1 protein expression and decreased Egr1-dependent transcription of IL2 in activated T cells. Our findings identify DNA-PKcs as a critical intermediary link between T cell activation and T cell fate and a novel phosphosite involved in regulating Egr1 activity.
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Affiliation(s)
- Zachary J Waldrip
- Division of Surgical Research, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Center for Translational Pediatric Research, Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Lyle Burdine
- Division of Surgical Research, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Department of Transplant Surgery, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - David K Harrison
- Division of Surgical Research, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Center for Translational Pediatric Research, Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Ana Clara Azevedo-Pouly
- Division of Surgical Research, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Center for Translational Pediatric Research, Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Olivia G Moffett
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Marie Schluterman Burdine
- Division of Surgical Research, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Center for Translational Pediatric Research, Arkansas Children's Research Institute, Little Rock, Arkansas, USA.
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18
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Delgado M, Washam CL, Urbaniak A, Heflin B, Storey AJ, Lan RS, Mackintosh SG, Tackett AJ, Byrum SD, Chambers TC. Phosphoproteomics Provides Novel Insights into the Response of Primary Acute Lymphoblastic Leukemia Cells to Microtubule Depolymerization in G1 Phase of the Cell Cycle. ACS Omega 2021; 6:24949-24959. [PMID: 34604676 PMCID: PMC8482483 DOI: 10.1021/acsomega.1c03936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Microtubule targeting agents (MTAs) have been used for the treatment of cancer for many decades and are among the most successful chemotherapeutic agents. However, their application and effectiveness are limited because of toxicity and resistance as well as a lack of knowledge of molecular mechanisms downstream of microtubule inhibition. Insights into key pathways that link microtubule disruption to cell death is critical for optimal use of these drugs, for defining biomarkers useful in patient stratification, and for informed design of drug combinations. Although MTAs characteristically induce death in mitosis, microtubule destabilizing agents such as vincristine also induce death directly in G1 phase in primary acute lymphoblastic leukemia (ALL) cells. Because many signaling pathways regulating cell survival and death involve changes in protein expression and phosphorylation, we undertook a comprehensive quantitative proteomic study of G1 phase ALL cells treated with vincristine. The results revealed distinct alterations associated with c-Jun N-terminal kinase signaling, anti-proliferative signaling, the DNA damage response, and cytoskeletal remodeling. Signals specifically associated with cell death were identified by pre-treatment with the CDK4/6 inhibitor palbociclib, which caused G1 arrest and precluded death induction. These results provide insights into signaling mechanisms regulating cellular responses to microtubule inhibition and provide a foundation for a better understanding of the clinical mechanisms of MTAs and for the design of novel drug combinations. The mass spectrometry proteomics data have been deposited to the PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) via the PRIDE partner repository with the data set identifier PXD027190 and 10.6019/PXD027190.
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Affiliation(s)
- Magdalena Delgado
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Charity L. Washam
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Arkansas
Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas 72202, United States
| | - Alicja Urbaniak
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Billie Heflin
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Aaron J. Storey
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Renny S. Lan
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Samuel G. Mackintosh
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Alan J. Tackett
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Arkansas
Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas 72202, United States
- Winthrop
P. Rockefeller Cancer Institute, 449 Jack Stephens Dr, Little Rock, Arkansas 72205, United
States
| | - Stephanie D. Byrum
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Arkansas
Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas 72202, United States
- Winthrop
P. Rockefeller Cancer Institute, 449 Jack Stephens Dr, Little Rock, Arkansas 72205, United
States
| | - Timothy C. Chambers
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Winthrop
P. Rockefeller Cancer Institute, 449 Jack Stephens Dr, Little Rock, Arkansas 72205, United
States
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19
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Ahn JH, Davis ES, Daugird TA, Zhao S, Quiroga IY, Uryu H, Li J, Storey AJ, Tsai YH, Keeley DP, Mackintosh SG, Edmondson RD, Byrum SD, Cai L, Tackett AJ, Zheng D, Legant WR, Phanstiel DH, Wang GG. Phase separation drives aberrant chromatin looping and cancer development. Nature 2021; 595:591-595. [PMID: 34163069 PMCID: PMC8647409 DOI: 10.1038/s41586-021-03662-5] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/21/2021] [Indexed: 01/05/2023]
Abstract
The development of cancer is intimately associated with genetic abnormalities that target proteins with intrinsically disordered regions (IDRs). In human haematological malignancies, recurrent chromosomal translocation of nucleoporin (NUP98 or NUP214) generates an aberrant chimera that invariably retains the nucleoporin IDR-tandemly dispersed repeats of phenylalanine and glycine residues1,2. However, how unstructured IDRs contribute to oncogenesis remains unclear. Here we show that IDRs contained within NUP98-HOXA9, a homeodomain-containing transcription factor chimera recurrently detected in leukaemias1,2, are essential for establishing liquid-liquid phase separation (LLPS) puncta of chimera and for inducing leukaemic transformation. Notably, LLPS of NUP98-HOXA9 not only promotes chromatin occupancy of chimera transcription factors, but also is required for the formation of a broad 'super-enhancer'-like binding pattern typically seen at leukaemogenic genes, which potentiates transcriptional activation. An artificial HOX chimera, created by replacing the phenylalanine and glycine repeats of NUP98 with an unrelated LLPS-forming IDR of the FUS protein3,4, had similar enhancing effects on the genome-wide binding and target gene activation of the chimera. Deeply sequenced Hi-C revealed that phase-separated NUP98-HOXA9 induces CTCF-independent chromatin loops that are enriched at proto-oncogenes. Together, this report describes a proof-of-principle example in which cancer acquires mutation to establish oncogenic transcription factor condensates via phase separation, which simultaneously enhances their genomic targeting and induces organization of aberrant three-dimensional chromatin structure during tumourous transformation. As LLPS-competent molecules are frequently implicated in diseases1,2,4-7, this mechanism can potentially be generalized to many malignant and pathological settings.
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Affiliation(s)
- Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy A Daugird
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Shuai Zhao
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Ivana Yoseli Quiroga
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hidetaka Uryu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jie Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Daniel P Keeley
- UNC Neuroscience Center and Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Deyou Zheng
- Departments of Genetics, Neurology, and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Wesley R Legant
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, and North Carolina State University, Raleigh, NC, USA
| | - Douglas H Phanstiel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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20
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Fan H, Guo Y, Tsai YH, Storey AJ, Kim A, Gong W, Edmondson RD, Mackintosh SG, Li H, Byrum SD, Tackett AJ, Cai L, Wang GG. A conserved BAH module within mammalian BAHD1 connects H3K27me3 to Polycomb gene silencing. Nucleic Acids Res 2021; 49:4441-4455. [PMID: 33823544 PMCID: PMC8096256 DOI: 10.1093/nar/gkab210] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/28/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
Trimethylation of histone H3 lysine 27 (H3K27me3) is important for gene silencing and imprinting, (epi)genome organization and organismal development. In a prevalent model, the functional readout of H3K27me3 in mammalian cells is achieved through the H3K27me3-recognizing chromodomain harbored within the chromobox (CBX) component of canonical Polycomb repressive complex 1 (cPRC1), which induces chromatin compaction and gene repression. Here, we report that binding of H3K27me3 by a Bromo Adjacent Homology (BAH) domain harbored within BAH domain-containing protein 1 (BAHD1) is required for overall BAHD1 targeting to chromatin and for optimal repression of the H3K27me3-demarcated genes in mammalian cells. Disruption of direct interaction between BAHD1BAH and H3K27me3 by point mutagenesis leads to chromatin remodeling, notably, increased histone acetylation, at its Polycomb gene targets. Mice carrying an H3K27me3-interaction-defective mutation of Bahd1BAH causes marked embryonic lethality, showing a requirement of this pathway for normal development. Altogether, this work demonstrates an H3K27me3-initiated signaling cascade that operates through a conserved BAH ‘reader’ module within BAHD1 in mammals.
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Affiliation(s)
- Huitao Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Arum Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Haitao Li
- Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, and Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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21
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Wang Y, Zhou J, Mackintosh SG, Du Y. RuvB-Like Protein 2 Interacts with the NS1 Protein of Influenza A Virus and Affects Apoptosis That Is Counterbalanced by Type I Interferons. Viruses 2021; 13:v13061038. [PMID: 34072766 PMCID: PMC8229658 DOI: 10.3390/v13061038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/12/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
The NS1 protein of influenza A virus (IAV) plays important roles in viral pathogenesis and host immune response. Through a proteomic approach, we have identified RuvB-like proteins 1 and 2 (RuvBL1 and RuvBL2) as interacting partners of the NS1 protein of IAVs. Infection of human lung A549 cells with A/PR/8/34 (PR8) virus resulted in reductions in the protein levels of RuvBL2 but not RuvBL1. Further studies with RuvBL2 demonstrated that the NS1-RuvBL2 interaction is RNA-independent, and RuvBL2 binds the RNA-binding domain of the NS1. Infection of interferon (IFN)-deficient Vero cells with wild-type or delNS1 PR8 virus reduced RuvBL2 protein levels and induced apoptosis; delNS1 virus caused more reductions in RuvBL2 protein levels and induced more apoptosis than did wild-type virus. Knockdown of RuvBL2 by siRNAs induced apoptosis and overexpression of RuvBL2 resulted in increased resistance to infection-induced apoptosis in Vero cells. These results suggest that a non-NS1 viral element or elements induce apoptosis by suppressing RuvBL2 protein levels, and the NS1 inhibits the non-NS1 viral element-induced apoptosis by maintaining RuvBL2 abundance in infected cells in the absence of IFN influence. In contrast to Vero cells, infection of IFN-competent A549 cells with PR8 virus caused reductions in RuvBL2 protein levels but did not induce apoptosis. Concomitantly, pretreatment of Vero cells with a recombinant IFN resulted in resistance to infection-induced apoptosis. These results demonstrate that the infection-induced, RuvBL2-regulated apoptosis in infected cells is counterbalanced by IFN survival signals. Our results reveal a novel mechanism underlying the infection-induced apoptosis that can be modulated by the NS1 and type I IFN signaling in IAV-infected cells.
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Affiliation(s)
- Yimeng Wang
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (Y.W.); (J.Z.)
| | - Jianhong Zhou
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (Y.W.); (J.Z.)
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Yuchun Du
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (Y.W.); (J.Z.)
- Correspondence: ; Tel.: +1-479-575-6944
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22
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Xu C, Tsai YH, Galbo PM, Gong W, Storey AJ, Xu Y, Byrum SD, Xu L, Whang YE, Parker JS, Mackintosh SG, Edmondson RD, Tackett AJ, Huang J, Zheng D, Earp HS, Wang GG, Cai L. Cistrome analysis of YY1 uncovers a regulatory axis of YY1:BRD2/4-PFKP during tumorigenesis of advanced prostate cancer. Nucleic Acids Res 2021; 49:4971-4988. [PMID: 33849067 PMCID: PMC8136773 DOI: 10.1093/nar/gkab252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Castration-resistant prostate cancer (CRPC) is a terminal disease and the molecular underpinnings of CRPC development need to be better understood in order to improve its treatment. Here, we report that a transcription factor Yin Yang 1 (YY1) is significantly overexpressed during prostate cancer progression. Functional and cistrome studies of YY1 uncover its roles in promoting prostate oncogenesis in vitro and in vivo, as well as sustaining tumor metabolism including the Warburg effect and mitochondria respiration. Additionally, our integrated genomics and interactome profiling in prostate tumor show that YY1 and bromodomain-containing proteins (BRD2/4) co-occupy a majority of gene-regulatory elements, coactivating downstream targets. Via gene loss-of-function and rescue studies and mutagenesis of YY1-bound cis-elements, we unveil an oncogenic pathway in which YY1 directly binds and activates PFKP, a gene encoding the rate-limiting enzyme for glycolysis, significantly contributing to the YY1-enforced Warburg effect and malignant growth. Altogether, this study supports a master regulator role for YY1 in prostate tumorigenesis and reveals a YY1:BRD2/4-PFKP axis operating in advanced prostate cancer with implications for therapy.
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Affiliation(s)
- Chenxi Xu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Phillip M Galbo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Yuemei Xu
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Pathology, Nanjing Drum Tower Hospital and The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Lingfan Xu
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Young E Whang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neurology and Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - H Shelton Earp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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23
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Li J, Galbo PM, Gong W, Storey AJ, Tsai YH, Yu X, Ahn JH, Guo Y, Mackintosh SG, Edmondson RD, Byrum SD, Farrar JE, He S, Cai L, Jin J, Tackett AJ, Zheng D, Wang GG. ZMYND11-MBTD1 induces leukemogenesis through hijacking NuA4/TIP60 acetyltransferase complex and a PWWP-mediated chromatin association mechanism. Nat Commun 2021; 12:1045. [PMID: 33594072 PMCID: PMC7886901 DOI: 10.1038/s41467-021-21357-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 01/22/2021] [Indexed: 12/26/2022] Open
Abstract
Recurring chromosomal translocation t(10;17)(p15;q21) present in a subset of human acute myeloid leukemia (AML) patients creates an aberrant fusion gene termed ZMYND11-MBTD1 (ZM); however, its function remains undetermined. Here, we show that ZM confers primary murine hematopoietic stem/progenitor cells indefinite self-renewal capability ex vivo and causes AML in vivo. Genomics profilings reveal that ZM directly binds to and maintains high expression of pro-leukemic genes including Hoxa, Meis1, Myb, Myc and Sox4. Mechanistically, ZM recruits the NuA4/Tip60 histone acetyltransferase complex to cis-regulatory elements, sustaining an active chromatin state enriched in histone acetylation and devoid of repressive histone marks. Systematic mutagenesis of ZM demonstrates essential requirements of Tip60 interaction and an H3K36me3-binding PWWP (Pro-Trp-Trp-Pro) domain for oncogenesis. Inhibitor of histone acetylation-'reading' bromodomain proteins, which act downstream of ZM, is efficacious in treating ZM-induced AML. Collectively, this study demonstrates AML-causing effects of ZM, examines its gene-regulatory roles, and reports an attractive mechanism-guided therapeutic strategy.
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MESH Headings
- Acetylation
- Animals
- Carcinogenesis
- Cell Cycle Proteins/chemistry
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Cell Proliferation
- Cell Transformation, Neoplastic
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/metabolism
- Co-Repressor Proteins/chemistry
- Co-Repressor Proteins/metabolism
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/metabolism
- Disease Models, Animal
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic
- Genome, Human
- HEK293 Cells
- Hematopoietic Stem Cells/metabolism
- Histones/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Lysine Acetyltransferase 5/metabolism
- Mice, Inbred BALB C
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Oncogene Proteins, Fusion/metabolism
- Protein Binding
- Protein Domains
- Transcription Factors/metabolism
- Mice
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Affiliation(s)
- Jie Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Phillip M Galbo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jason E Farrar
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Shenghui He
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neurology and Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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24
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Martinez Barrera S, Byrum S, Mackintosh SG, Kozubowski L. Registered report protocol: Quantitative analysis of septin Cdc10-associated proteome in Cryptococcus neoformans. PLoS One 2020; 15:e0242381. [PMID: 33315917 PMCID: PMC7735571 DOI: 10.1371/journal.pone.0242381] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/29/2020] [Indexed: 11/19/2022] Open
Abstract
Cryptococcus neoformans is a pathogenic basidiomycetous yeast that primarily infects immunocompromised individuals. C. neoformans can thrive during infections due to its three main virulence-related characteristics: the ability to grow at host temperature (37°C), formation of carbohydrate capsule, and its ability to produce melanin. C. neoformans strains lacking septin proteins Cdc3 or Cdc12 are viable at 25°C; however, they fail to proliferate at 37°C and are avirulent in the murine model of infection. The basis of septin contribution to growth at host temperature remains unknown. Septins are a family of conserved filament-forming GTPases with roles in cytokinesis and morphogenesis. In the model organism Saccharomyces cerevisiae septins are essential. S. cerevisiae septins form a higher order complex at the mother-bud neck to scaffold over 80 proteins, including those involved in cell wall organization, cell polarity, and cell cycle control. In C. neoformans, septins also form a complex at the mother-bud neck but the septin interacting proteome in this species remains largely unknown. Moreover, it remains possible that septins play other roles important for high temperature stress that are independent of their established role in cytokinesis. Therefore, we propose to perform a global analysis of septin Cdc10 binding partners in C. neoformans, including those that are specific to high temperature stress. This analysis will shed light on the underlying mechanism of survival of this pathogenic yeast during infection and can potentially lead to the discovery of novel drug targets.
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Affiliation(s)
- Stephani Martinez Barrera
- Department of Genetics and Biochemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC, United States of America
| | - Stephanie Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Lukasz Kozubowski
- Department of Genetics and Biochemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC, United States of America
- * E-mail:
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25
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Vazquez JH, Clemens MM, Allard FD, Yee EU, Kennon-McGill S, Mackintosh SG, Jaeschke H, Hambuchen MD, McGill MR. Identification of Serum Biomarkers to Distinguish Hazardous and Benign Aminotransferase Elevations. Toxicol Sci 2020; 173:244-254. [PMID: 31651977 DOI: 10.1093/toxsci/kfz222] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The standard circulating biomarker of liver injury in both clinical settings and drug safety testing is alanine aminotransferase (ALT). However, ALT elevations sometimes lack specificity for tissue damage. To identify novel serum biomarkers with greater specificity for injury, we combined unique animal models with untargeted proteomics, followed by confirmation with immunoblotting. Using proteomics, we identified 109 proteins in serum from mice with acetaminophen (APAP)-induced liver injury that were not detectable in serum from mice with benign ALT elevations due to high-dose dexamethasone (Dex). We selected 4 (alcohol dehydrogenase 1A1 [Aldh1a1], aldehyde dehydrogenase 1 [Adh1], argininosuccinate synthetase 1 [Ass1], and adenosylhomocysteinase [Ahcy]) with high levels for further evaluation. Importantly, all 4 were specific for injury when using immunoblots to compare serum from Dex-treated mice and mice with similar lower ALT elevations due to milder models of APAP or bromobenzene-induced liver injury. Immunoblotting for ALDH1A1, ADH1, and ASS1 in serum from APAP overdose patients without liver injury and APAP overdose patients with mild liver injury revealed that these candidate biomarkers can be detected in humans with moderate liver injury as well. Interestingly, further experiments with serum from rats with bile duct ligation-induced liver disease indicated that Aldh1a1 and Adh1 are not detectable in serum in cholestasis and may therefore be specific for hepatocellular injury and possibly even drug-induced liver injury, in particular. Overall, our results strongly indicate that ALDH1A1, ADH1, and ASS1 are promising specific biomarkers for liver injury. Adoption of these biomarkers could improve preapproval drug safety assessment.
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Affiliation(s)
- Joel H Vazquez
- Department of Pharmacology and Toxicology.,Graduate Program in Interdisciplinary Biomedical Sciences
| | - Melissa M Clemens
- Department of Pharmacology and Toxicology.,Graduate Program in Interdisciplinary Biomedical Sciences
| | - Felicia D Allard
- Department of Pathology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Eric U Yee
- Department of Pathology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Stefanie Kennon-McGill
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health
| | - Samuel G Mackintosh
- Department of Biochemistry, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Hartmut Jaeschke
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Michael D Hambuchen
- Department of Pharmaceutical Sciences and Research, School of Pharmacy, Marshall University, Huntington, West Virginia 25701
| | - Mitchell R McGill
- Department of Pharmacology and Toxicology.,Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health
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26
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Koss B, Shields BD, Taylor EM, Storey AJ, Byrum SD, Gies AJ, Washam CL, Choudhury SR, Hyun Ahn J, Uryu H, Williams JB, Krager KJ, Chiang TC, Mackintosh SG, Edmondson RD, Aykin-Burns N, Gajewski TF, Wang GG, Tackett AJ. Epigenetic Control of Cdkn2a.Arf Protects Tumor-Infiltrating Lymphocytes from Metabolic Exhaustion. Cancer Res 2020; 80:4707-4719. [PMID: 33004350 PMCID: PMC7642172 DOI: 10.1158/0008-5472.can-20-0524] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/04/2020] [Accepted: 08/28/2020] [Indexed: 01/06/2023]
Abstract
T-cell exhaustion in cancer is linked to poor clinical outcomes, where evidence suggests T-cell metabolic changes precede functional exhaustion. Direct competition between tumor-infiltrating lymphocytes (TIL) and cancer cells for metabolic resources often renders T cells dysfunctional. Environmental stress produces epigenome remodeling events within TIL resulting from loss of the histone methyltransferase EZH2. Here, we report an epigenetic mechanism contributing to the development of metabolic exhaustion in TIL. A multiomics approach revealed a Cdkn2a.Arf-mediated, p53-independent mechanism by which EZH2 inhibition leads to mitochondrial dysfunction and the resultant exhaustion. Reprogramming T cells to express a gain-of-function EZH2 mutant resulted in an enhanced ability of T cells to inhibit tumor growth in vitro and in vivo. Our data suggest that manipulation of T-cell EZH2 within the context of cellular therapies may yield lymphocytes that are able to withstand harsh tumor metabolic environments and collateral pharmacologic insults. SIGNIFICANCE: These findings demonstrate that manipulation of T-cell EZH2 in cellular therapies may yield cellular products able to withstand solid tumor metabolic-deficient environments. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/21/4707/F1.large.jpg.
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Affiliation(s)
- Brian Koss
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Bradley D Shields
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Erin M Taylor
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Allen J Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Charity L Washam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Samrat Roy Choudhury
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Hidetaka Uryu
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Jason B Williams
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Kimberly J Krager
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Tung-Chin Chiang
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Rick D Edmondson
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Nukhet Aykin-Burns
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Thomas F Gajewski
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas.
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Arkansas Children's Research Institute, Little Rock, Arkansas
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27
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Koss B, Shields BD, Taylor EM, Storey AJ, Byrum SD, Gies AJ, Washam CL, Choudhury SR, Ahn JH, Uryu H, Krager KJ, Chiang TC, Mackintosh SG, Edmondson RD, Aykin-Burns N, Wang GG, Tackett AJ. Abstract 1029: Epigenetic control of tumor-infiltrating lymphocyte metabolic-exhaustion. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Direct competition between tumor-infiltrating lymphocytes and cancer cells for metabolic resources often renders T cells dysfunctional. It is becoming clearer that T cell metabolic changes can precede functional exhaustion. In the case of solid tumors, the driving force of this dysfunction is thought to be a result of inhibitory metabolism (e.g. glucose deprivation and mitochondrial dysfunction). The mechanisms connecting inhibitory metabolism and T cell metabolic exhaustion are largely unknown. Interestingly, T cells undergo a loss of the histone methyltransferase EZH2 (H3K27me3) during tumor infiltration. Methyltransferases, like EZH2, depend on mitochondria to supply S-Adenosyl-L-Methionine (SAM), the primary methyl donor. We sought to determine if there was a link between EZH2 and mitochondrial function. In this work, we utilized highly specific EZH2 inhibitors to model acute inhibition of EZH2 in CD8+ and CD4+ T cells. Taking an unbiased, multi-omics approach (proteomics, RNAseq, ChIPseq) we fully interrogate the downstream consequences of EZH2 inhibition in T cells. The loss of H3K27me3 does indeed lead to an induction of mitochondrial dysfunction, which in turn, drives a dependency on glycolytic metabolism and sensitivity to glucose withdrawal. The metabolic shift phenotype was confirmed using extracellular metabolic flux analysis. In T cells, we found the loss of H3K27me3 repression of the Cdkn2aArf locus to be a major contributor to mitochondrial dysfunction, independent of the canonical role to stabilize p53. Furthermore, we show Arf-/- mice are resistant to EZH2-inhibition induced mitochondrial dysfunction. Reprogramming tumor-specific T cells to exogenously express a gain-of-function EZH2 mutant (Y641F) resulted in an enhanced ability of T cells to inhibit solid tumor growth. This work demonstrates the potential for manipulation of EZH2 in cellular therapies for solid tumors with harsh metabolic conditions and sheds light on the dynamic interplay of epigenetics and metabolic sufficiency.
Citation Format: Brian Koss, Bradley D. Shields, Erin M. Taylor, Aaron J. Storey, Stephanie D. Byrum, Allen J. Gies, Charity L. Washam, Samrat Roy Choudhury, Jeong Hyun Ahn, Hidetaka Uryu, Kimberly J. Krager, Tung-Chin Chiang, Samuel G. Mackintosh, Rick D. Edmondson, Nukhet Aykin-Burns, Gang Greg Wang, Alan J. Tackett. Epigenetic control of tumor-infiltrating lymphocyte metabolic-exhaustion [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1029.
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Affiliation(s)
- Brian Koss
- 1University of Arkansas for Medical Sciences, Little Rock, AR
| | | | - Erin M. Taylor
- 1University of Arkansas for Medical Sciences, Little Rock, AR
| | - Aaron J. Storey
- 1University of Arkansas for Medical Sciences, Little Rock, AR
| | | | - Allen J. Gies
- 1University of Arkansas for Medical Sciences, Little Rock, AR
| | | | | | - Jeong Hyun Ahn
- 2University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Hidetaka Uryu
- 2University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | | | | | | | | | | | - Gang Greg Wang
- 2University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Alan J. Tackett
- 1University of Arkansas for Medical Sciences, Little Rock, AR
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28
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Zhang L, Yao Y, Zhang S, Liu Y, Guo H, Ahmed M, Bell T, Zhang H, Han G, Lorence E, Badillo M, Zhou S, Sun Y, Di Francesco ME, Feng N, Haun R, Lan R, Mackintosh SG, Mao X, Song X, Zhang J, Pham LV, Lorenzi PL, Marszalek J, Heffernan T, Draetta G, Jones P, Futreal A, Nomie K, Wang L, Wang M. Metabolic reprogramming toward oxidative phosphorylation identifies a therapeutic target for mantle cell lymphoma. Sci Transl Med 2020; 11:11/491/eaau1167. [PMID: 31068440 DOI: 10.1126/scitranslmed.aau1167] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 11/02/2018] [Accepted: 03/29/2019] [Indexed: 12/30/2022]
Abstract
Metabolic reprogramming is linked to cancer cell growth and proliferation, metastasis, and therapeutic resistance in a multitude of cancers. Targeting dysregulated metabolic pathways to overcome resistance, an urgent clinical need in all relapsed/refractory cancers, remains difficult. Through genomic analyses of clinical specimens, we show that metabolic reprogramming toward oxidative phosphorylation (OXPHOS) and glutaminolysis is associated with therapeutic resistance to the Bruton's tyrosine kinase inhibitor ibrutinib in mantle cell lymphoma (MCL), a B cell lymphoma subtype with poor clinical outcomes. Inhibition of OXPHOS with a clinically applicable small molecule, IACS-010759, which targets complex I of the mitochondrial electron transport chain, results in marked growth inhibition in vitro and in vivo in ibrutinib-resistant patient-derived cancer models. This work suggests that targeting metabolic pathways to subvert therapeutic resistance is a clinically viable approach to treat highly refractory malignancies.
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Affiliation(s)
- Liang Zhang
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yixin Yao
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Liu
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Guo
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Makhdum Ahmed
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Taylor Bell
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Zhang
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangchun Han
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elizabeth Lorence
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria Badillo
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shouhao Zhou
- Department of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuting Sun
- Institute for Applied Cancer Science and Center for Co-Clinical Trials, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - M Emilia Di Francesco
- Institute for Applied Cancer Science and Center for Co-Clinical Trials, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ningping Feng
- Institute for Applied Cancer Science and Center for Co-Clinical Trials, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Randy Haun
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Renny Lan
- Department of Biochemistry and Molecular Biology and Proteomics Core Facility, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology and Proteomics Core Facility, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xizeng Mao
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xingzhi Song
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lan V Pham
- Department of Hematopathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philip L Lorenzi
- Proteomics and Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joseph Marszalek
- Institute for Applied Cancer Science and Center for Co-Clinical Trials, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tim Heffernan
- Institute for Applied Cancer Science and Center for Co-Clinical Trials, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Giulio Draetta
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Institute for Applied Cancer Science and Center for Co-Clinical Trials, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philip Jones
- Institute for Applied Cancer Science and Center for Co-Clinical Trials, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew Futreal
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Krystle Nomie
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Michael Wang
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. .,Department of Stem Cell Transplantation and Cellular Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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29
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Storey AJ, Naceanceno KS, Lan RS, Washam CL, Orr LM, Mackintosh SG, Tackett AJ, Edmondson RD, Wang Z, Li HY, Frett B, Kendrick S, Byrum SD. ProteoViz: a tool for the analysis and interactive visualization of phosphoproteomics data. Mol Omics 2020; 16:316-326. [PMID: 32347222 DOI: 10.1039/c9mo00149b] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Quantitative proteomics generates large datasets with increasing depth and quantitative information. With the advance of mass spectrometry and increasingly larger data sets, streamlined methodologies and tools for analysis and visualization of phosphoproteomics are needed both at the protein and modified peptide levels. To assist in addressing this need, we developed ProteoViz, which includes a set of R scripts that perform normalization and differential expression analysis of both the proteins and enriched phosphorylated peptides, and identify sequence motifs, kinases, and gene set enrichment pathways. The tool generates interactive visualization plots that allow users to interact with the phosphoproteomics results and quickly identify proteins and phosphorylated peptides of interest for their biological study. The tool also links significant phosphosites with sequence motifs and pathways that will help explain the experimental conditions and guide future experiments. Here, we present the workflow and demonstrate its functionality by analyzing a phosphoproteomic data set from two lymphoma cell lines treated with kinase inhibitors. The scripts and data are freely available at and via the ProteomeXchange with identifier PXD015606.
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Affiliation(s)
- Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
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30
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Chua XY, Mensah T, Aballo T, Mackintosh SG, Edmondson RD, Salomon AR. Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome. Mol Cell Proteomics 2020; 19:730-743. [PMID: 32071147 PMCID: PMC7124467 DOI: 10.1074/mcp.tir119.001865] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/07/2020] [Indexed: 01/08/2023] Open
Abstract
Dynamic tyrosine phosphorylation is fundamental to a myriad of cellular processes. However, the inherently low abundance of tyrosine phosphorylation in the proteome and the inefficient enrichment of phosphotyrosine(pTyr)-containing peptides has led to poor pTyr peptide identification and quantitation, critically hindering researchers' ability to elucidate signaling pathways regulated by tyrosine phosphorylation in systems where cellular material is limited. The most popular approaches to wide-scale characterization of the tyrosine phosphoproteome use pTyr enrichment with pan-specific, anti-pTyr antibodies from a large amount of starting material. Methods that decrease the amount of starting material and increase the characterization depth of the tyrosine phosphoproteome while maintaining quantitative accuracy and precision would enable the discovery of tyrosine phosphorylation networks in rarer cell populations. To achieve these goals, the BOOST (Broad-spectrum Optimization Of Selective Triggering) method leveraging the multiplexing capability of tandem mass tags (TMT) and the use of pervanadate (PV) boost channels (cells treated with the broad-spectrum tyrosine phosphatase inhibitor PV) selectively increased the relative abundance of pTyr-containing peptides. After PV boost channels facilitated selective fragmentation of pTyr-containing peptides, TMT reporter ions delivered accurate quantitation of each peptide for the experimental samples while the quantitation from PV boost channels was ignored. This method yielded up to 6.3-fold boost in pTyr quantification depth of statistically significant data derived from contrived ratios, compared with TMT without PV boost channels or intensity-based label-free (LF) quantitation while maintaining quantitative accuracy and precision, allowing quantitation of over 2300 unique pTyr peptides from only 1 mg of T cell receptor-stimulated Jurkat T cells. The BOOST strategy can potentially be applied in analyses of other post-translational modifications where treatments that broadly elevate the levels of those modifications across the proteome are available.
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Affiliation(s)
- Xien Yu Chua
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island
| | - Theresa Mensah
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Timothy Aballo
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Arthur R Salomon
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.
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31
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Dimori M, Heard-Lipsmeyer ME, Byrum SD, Mackintosh SG, Kurten RC, Carroll JL, Morello R. Respiratory defects in the CrtapKO mouse model of osteogenesis imperfecta. Am J Physiol Lung Cell Mol Physiol 2020; 318:L592-L605. [PMID: 32022592 PMCID: PMC7191481 DOI: 10.1152/ajplung.00313.2019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Respiratory disease is a leading cause of mortality in patients with osteogenesis imperfecta (OI), a connective tissue disease that causes severely reduced bone mass and is most commonly caused by dominant mutations in type I collagen genes. Previous studies proposed that impaired respiratory function in OI patients was secondary to skeletal deformities; however, recent evidence suggests the existence of a primary lung defect. Here, we analyzed the lung phenotype of Crtap knockout (KO) mice, a mouse model of recessive OI. While we confirm changes in the lung parenchyma that are reminiscent of emphysema, we show that CrtapKO lung fibroblasts synthesize type I collagen with altered posttranslation modifications consistent with those observed in bone and skin. Unrestrained whole body plethysmography showed a significant decrease in expiratory time, resulting in an increased ratio of inspiratory time over expiratory time and a concomitant increase of the inspiratory duty cycle in CrtapKO compared with WT mice. Closed-chest measurements using the forced oscillation technique showed increased respiratory system elastance, decreased respiratory system compliance, and increased tissue damping and elasticity in CrtapKO mice compared with WT. Pressure-volume curves showed significant differences in lung volumes and in the shape of the curves between CrtapKO mice and WT mice, with and without adjustment for body weight. This is the first evidence that collagen defects in OI cause primary changes in lung parenchyma and several respiratory parameters and thus negatively impact lung function.
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Affiliation(s)
- Milena Dimori
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Melissa E Heard-Lipsmeyer
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Richard C Kurten
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - John L Carroll
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Roy Morello
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Department of Orthopaedic Surgery, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Division of Genetics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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32
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Storey AJ, Hardman RE, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA. Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags. J Proteome Res 2020; 19:1183-1195. [PMID: 32027144 DOI: 10.1021/acs.jproteome.9b00704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells respond to environmental perturbations and insults through modulating protein abundance and function. However, the majority of studies have focused on changes in RNA abundance because quantitative transcriptomics has historically been more facile than quantitative proteomics. Modern Orbitrap mass spectrometers now provide sensitive and deep proteome coverage, allowing direct, global quantification of not only protein abundance but also post-translational modifications (PTMs) that regulate protein activity. We implemented and validated using the well-characterized heat shock response of budding yeast, a tandem mass tagging (TMT), triple-stage mass spectrometry (MS3) strategy to measure global changes in the proteome during the yeast heat shock response over nine time points. We report that basic-pH, ultra-high performance liquid chromatography (UPLC) fractionation of tryptic peptides yields superfractions of minimal redundancy, a crucial requirement for deep coverage and quantification by subsequent LC-MS3. We quantified 2275 proteins across three biological replicates and found that differential expression peaked near 90 min following heat shock (with 868 differentially expressed proteins at 5% false discovery rate). The sensitivity of the approach also allowed us to detect changes in the relative abundance of ubiquitination and phosphorylation PTMs over time. Remarkably, relative quantification of post-translationally modified peptides revealed striking evidence of regulation of the heat shock response by protein PTMs. These data demonstrate that the high precision of TMT-MS3 enables peptide-level quantification of samples, which can reveal important regulation of protein abundance and regulatory PTMs under various experimental conditions.
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Affiliation(s)
- Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rebecca E Hardman
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas 72701, United States.,Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rick D Edmondson
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Wayne P Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Jeffrey A Lewis
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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33
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Ramirez AM, Byrum SD, Beenken KE, Washam C, Edmondson RD, Mackintosh SG, Spencer HJ, Tackett AJ, Smeltzer MS. Exploiting Correlations between Protein Abundance and the Functional Status of saeRS and sarA To Identify Virulence Factors of Potential Importance in the Pathogenesis of Staphylococcus aureus Osteomyelitis. ACS Infect Dis 2020; 6:237-249. [PMID: 31722523 PMCID: PMC7294808 DOI: 10.1021/acsinfecdis.9b00291] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We used a murine model of postsurgical osteomyelitis (OM) to evaluate the relative virulence of the Staphylococcus aureus strain LAC and five isogenic variants that differ in the functional status of saeRS and sarA relative to each other. LAC and a variant in which saeRS activity is increased (saeC) were comparably virulent to each other, while ΔsaeRS, ΔsarA, ΔsaeRS/ΔsarA, and saeC/ΔsarA mutants were all attenuated to a comparable degree. Phenotypic comparisons including a mass-based proteomics approach that allowed us to assess the number and abundance of full-length proteins suggested that mutation of saeRS attenuates virulence in our OM model owing primarily to the decreased production of S. aureus virulence factors, while mutation of sarA does so owing to protease-mediated degradation of these same virulence factors. This was confirmed by demonstrating that eliminating protease production restored virulence to a greater extent in a LAC sarA mutant than in the isogenic saeRS mutant. Irrespective of the mechanism involved, mutation of saeRS or sarA was shown to result in reduced accumulation of virulence factors of potential importance. Thus, using our proteomics approach we correlated the abundance of specific proteins with virulence in these six strains and identified 14 proteins that were present in a significantly increased amount (log2 ≥ 5.0) in both virulent strains by comparison to all four attenuated strains. We examined biofilm formation and virulence in our OM model using a LAC mutant unable to produce one of these 14 proteins, specifically staphylocoagulase. The results confirmed that mutation of coa limits biofilm formation and, to a lesser extent, virulence in our OM model, although in both cases the limitation was reduced by comparison to the isogenic sarA mutant.
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Affiliation(s)
- Aura M. Ramirez
- Department of Microbiology
and Immunology, College of Medicine, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 511, Little Rock, Arkansas 72205, United States
| | - Stephanie D. Byrum
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 516, Little Rock, Arkansas 72205, United States,Arkansas
Children’s Research Institute, 1 Children’s Way, Little Rock, Arkansas 72202, United States
| | - Karen E. Beenken
- Department of Microbiology
and Immunology, College of Medicine, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 511, Little Rock, Arkansas 72205, United States
| | - Charity Washam
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 516, Little Rock, Arkansas 72205, United States,Arkansas
Children’s Research Institute, 1 Children’s Way, Little Rock, Arkansas 72202, United States
| | - Rick D. Edmondson
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 516, Little Rock, Arkansas 72205, United States
| | - Samuel G. Mackintosh
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 516, Little Rock, Arkansas 72205, United States
| | - Horace J. Spencer
- Department of Biostatistics, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Little Rock, Arkansas 72205, United States
| | - Alan J. Tackett
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 516, Little Rock, Arkansas 72205, United States,Arkansas
Children’s Research Institute, 1 Children’s Way, Little Rock, Arkansas 72202, United States
| | - Mark S. Smeltzer
- Department of Microbiology
and Immunology, College of Medicine, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 511, Little Rock, Arkansas 72205, United States,Department
of Orthopaedic Surgery, University of Arkansas
for Medical Sciences, 4301 W. Markham Street, Slot 531, Little Rock, Arkansas 72205, United States,Phone: 501-686-7958. E-mail:
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34
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Ren Z, Ahn JH, Liu H, Tsai YH, Bhanu NV, Koss B, Allison DF, Ma A, Storey AJ, Wang P, Mackintosh SG, Edmondson RD, Groen RWJ, Martens AC, Garcia BA, Tackett AJ, Jin J, Cai L, Zheng D, Wang GG. PHF19 promotes multiple myeloma tumorigenicity through PRC2 activation and broad H3K27me3 domain formation. Blood 2019; 134:1176-1189. [PMID: 31383640 PMCID: PMC6776795 DOI: 10.1182/blood.2019000578] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/24/2019] [Indexed: 12/31/2022] Open
Abstract
Dysregulation of polycomb repressive complex 2 (PRC2) promotes oncogenesis partly through its enzymatic function for inducing trimethylation of histone H3 lysine 27 (H3K27me3). However, it remains to be determined how PRC2 activity is regulated in normal and diseased settings. We here report a PRC2-associated cofactor, PHD finger protein 19 (PHF19; also known as polycomb-like 3), as a crucial mediator of tumorigenicity in multiple myeloma (MM). Overexpression and/or genomic amplification of PHF19 is found associated with malignant progression of MM and plasma cell leukemia, correlating to worse treatment outcomes. Using various MM models, we demonstrated a critical requirement of PHF19 for tumor growth in vitro and in vivo. Mechanistically, PHF19-mediated oncogenic effect relies on its PRC2-interacting and chromatin-binding functions. Chromatin immunoprecipitation followed by sequencing profiling showed a critical role for PHF19 in maintaining the H3K27me3 landscape. PHF19 depletion led to loss of broad H3K27me3 domains, possibly due to impaired H3K27me3 spreading from cytosine guanine dinucleotide islands, which is reminiscent to the reported effect of an "onco"-histone mutation, H3K27 to methionine (H3K27M). RNA-sequencing-based transcriptome profiling in MM lines also demonstrated a requirement of PHF19 for optimal silencing of PRC2 targets, which include cell cycle inhibitors and interferon-JAK-STAT signaling genes critically involved in tumor suppression. Correlation studies using patient sample data sets further support a clinical relevance of the PHF19-regulated pathways. Lastly, we show that MM cells are generally sensitive to PRC2 inhibitors. Collectively, this study demonstrates that PHF19 promotes MM tumorigenesis through enhancing H3K27me3 deposition and PRC2's gene-regulatory functions, lending support for PRC2 blockade as a means for MM therapeutics.
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Affiliation(s)
- Zhihong Ren
- Lineberger Comprehensive Cancer Center and
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center and
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Hequn Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
| | | | - Natarajan V Bhanu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Brian Koss
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - David F Allison
- Lineberger Comprehensive Cancer Center and
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Anqi Ma
- Center for Chemical Biology and Drug Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Ping Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Richard W J Groen
- Department of Hematology, Amsterdam UMC, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Anton C Martens
- Department of Hematology, Amsterdam UMC, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR
- Arkansas Children's Research Institute and UAMS Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Jian Jin
- Center for Chemical Biology and Drug Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ling Cai
- Lineberger Comprehensive Cancer Center and
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
- Department of Neuroscience and
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY; and
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center and
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
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35
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Cragle CE, MacNicol MC, Byrum SD, Hardy LL, Mackintosh SG, Richardson WA, Gray NK, Childs GV, Tackett AJ, MacNicol AM. Musashi interaction with poly(A)-binding protein is required for activation of target mRNA translation. J Biol Chem 2019; 294:10969-10986. [PMID: 31152063 PMCID: PMC6635449 DOI: 10.1074/jbc.ra119.007220] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/09/2019] [Indexed: 12/21/2022] Open
Abstract
The Musashi family of mRNA translational regulators controls both physiological and pathological stem cell self-renewal primarily by repressing target mRNAs that promote differentiation. In response to differentiation cues, Musashi can switch from a repressor to an activator of target mRNA translation. However, the molecular events that distinguish Musashi-mediated translational activation from repression are not understood. We have previously reported that Musashi function is required for the maturation of Xenopus oocytes and specifically for translational activation of specific dormant maternal mRNAs. Here, we employed MS to identify cellular factors necessary for Musashi-dependent mRNA translational activation. We report that Musashi1 needs to associate with the embryonic poly(A)-binding protein (ePABP) or the canonical somatic cell poly(A)-binding protein PABPC1 for activation of Musashi target mRNA translation. Co-immunoprecipitation studies demonstrated an increased Musashi1 interaction with ePABP during oocyte maturation. Attenuation of endogenous ePABP activity severely compromised Musashi function, preventing downstream signaling and blocking oocyte maturation. Ectopic expression of either ePABP or PABPC1 restored Musashi-dependent mRNA translational activation and maturation of ePABP-attenuated oocytes. Consistent with these Xenopus findings, PABPC1 remained associated with Musashi under conditions of Musashi target mRNA de-repression and translation during mammalian stem cell differentiation. Because association of Musashi1 with poly(A)-binding proteins has previously been implicated only in repression of Musashi target mRNAs, our findings reveal novel context-dependent roles for the interaction of Musashi with poly(A)-binding protein family members in response to extracellular cues that control cell fate.
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Affiliation(s)
- Chad E Cragle
- Department of Neurobiology and Developmental Sciences
| | - Melanie C MacNicol
- Department of Neurobiology and Developmental Sciences,; Center for Translational Neuroscience
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology,; Arkansas Children's Research Institute
| | - Linda L Hardy
- Department of Neurobiology and Developmental Sciences
| | | | - William A Richardson
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, Scotland, United Kingdom
| | - Nicola K Gray
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, Scotland, United Kingdom
| | - Gwen V Childs
- Department of Neurobiology and Developmental Sciences,; Center for Translational Neuroscience
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology,; Arkansas Children's Research Institute
| | - Angus M MacNicol
- Department of Neurobiology and Developmental Sciences,; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and.
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36
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Gao J, Byrd AK, Zybailov BL, Marecki JC, Guderyon MJ, Edwards AD, Chib S, West KL, Waldrip ZJ, Mackintosh SG, Gao Z, Putnam AA, Jankowsky E, Raney KD. DEAD-box RNA helicases Dbp2, Ded1 and Mss116 bind to G-quadruplex nucleic acids and destabilize G-quadruplex RNA. Chem Commun (Camb) 2019; 55:4467-4470. [PMID: 30855040 DOI: 10.1039/c8cc10091h] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We identified 29 G-quadruplex binding proteins by affinity purification and quantitative LC-MS/MS. We demonstrated that the DEAD-box RNA helicases Dbp2, Ded1 and Mss116 preferentially bind to G-quadruplex nucleic acids in vitro and destabilize RNA quadruplexes, suggesting new potential roles for these helicases in disruption of quadruplex structures in RNA.
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Affiliation(s)
- Jun Gao
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, Arkansas 72205, USA.
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37
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Shields BD, Koss B, Taylor EM, Storey AJ, West KL, Byrum SD, Mackintosh SG, Edmondson R, Mahmoud F, Shalin SC, Tackett AJ. Loss of E-Cadherin Inhibits CD103 Antitumor Activity and Reduces Checkpoint Blockade Responsiveness in Melanoma. Cancer Res 2019; 79:1113-1123. [PMID: 30674537 PMCID: PMC6420873 DOI: 10.1158/0008-5472.can-18-1722] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 11/04/2018] [Accepted: 01/18/2019] [Indexed: 11/16/2022]
Abstract
Identifying controlling features of responsiveness to checkpoint blockade therapies is an urgent goal in oncology research. Our group and others have previously shown melanoma tumors resistant to checkpoint blockade display features of mesenchymal transition, including E-cadherin loss. Here, we present the first in vivo evidence that E-cadherin from tumor cells facilitate immune attack, using a B16F10 melanoma mouse model in which E-cadherin is exogenously expressed (B16.Ecad). We find, compared with vector control, B16.Ecad exhibits delayed tumor growth, reduced metastatic potential, and increased overall survival in vivo. Transplantation of B16.Ecad into Rag1-/- and CD103-/- mice abrogated the tumor growth delay. This indicates the anti-melanoma response against B16.Ecad is both immune and CD103+ mediated. Moreover, B16.Ecad showed increased responsiveness to combination immune checkpoint blockade (ICB) compared with vector control. This work establishes a rationale for ICB responses observed in high E-cadherin-expressing tumors and suggests therapeutic advancement through amplifying CD103+ immune cell subsets.Significance: These findings identify the mechanism behind checkpoint blockade resistance observed in melanoma that has undergone mesenchymal transition and suggest activation of CD103+ immune cells as a therapeutic strategy against other E-cadherin-expressing malignancies.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/6/1113/F1.large.jpg.
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Affiliation(s)
- Bradley D. Shields
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Brian Koss
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Erin M. Taylor
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Aaron J. Storey
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Kirk L. West
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Stephanie D. Byrum
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA.,Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas, 72202, USA
| | - Samuel G. Mackintosh
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Rick Edmondson
- College of Medicine, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Fade Mahmoud
- College of Medicine, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Sara C. Shalin
- Department of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Alan J. Tackett
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA.,Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas, 72202, USA,Corresponding author: Alan J. Tackett, PhD, Professor of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA, , Office: (501)686-8152, FAX: (501)686-8169
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38
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West KL, Byrum SD, Mackintosh SG, Edmondson RD, Taverna SD, Tackett AJ. Proteomic characterization of the arsenic response locus in S. cerevisiae. Epigenetics 2019; 14:130-145. [PMID: 30739529 DOI: 10.1080/15592294.2019.1580110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Arsenic exposure is a global health problem. Millions of people encounter arsenic through contaminated drinking water, consumption, and inhalation. The arsenic response locus in budding yeast is responsible for the detoxification of arsenic and its removal from the cell. This locus constitutes a conserved pathway ranging from prokaryotes to higher eukaryotes. The goal of this study was to identify how transcription from the arsenic response locus is regulated in an arsenic dependent manner. An affinity enrichment strategy called CRISPR-Chromatin Affinity Purification with Mass Spectrometry (CRISPR-ChAP-MS) was used, which provides for the proteomic characterization of a targeted locus. CRISPR-ChAP-MS was applied to the promoter regions of the activated arsenic response locus and uncovered 40 nuclear-annotated proteins showing enrichment. Functional assays identified the histone acetyltransferase SAGA and the chromatin remodelling complex SWI/SNF to be required for activation of the locus. Furthermore, SAGA and SWI/SNF were both found to specifically organize the chromatin structure at the arsenic response locus for activation of gene transcription. This study provides the first proteomic characterization of an arsenic response locus and key insight into the mechanisms of transcriptional activation that are necessary for detoxification of arsenic from the cell.
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Affiliation(s)
- Kirk L West
- a Department of Biochemistry and Molecular Biology , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Stephanie D Byrum
- a Department of Biochemistry and Molecular Biology , University of Arkansas for Medical Sciences , Little Rock , AR , USA.,b Arkansas Children's Research Institute , Little Rock , AR , USA
| | - Samuel G Mackintosh
- a Department of Biochemistry and Molecular Biology , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Rick D Edmondson
- c College of Medicine , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Sean D Taverna
- d Department of Pharmacology and Molecular Sciences , The Johns Hopkins University School of Medicine , Baltimore , MD , USA.,e Center for Epigenetics , The Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Alan J Tackett
- a Department of Biochemistry and Molecular Biology , University of Arkansas for Medical Sciences , Little Rock , AR , USA.,b Arkansas Children's Research Institute , Little Rock , AR , USA
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39
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Zybailov BL, Glazko GV, Rahmatallah Y, Andreyev DS, McElroy T, Karaduta O, Byrum SD, Orr L, Tackett AJ, Mackintosh SG, Edmondson RD, Kieffer DA, Martin RJ, Adams SH, Vaziri ND, Arthur JM. Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats. PLoS One 2019; 14:e0199274. [PMID: 30699108 PMCID: PMC6353070 DOI: 10.1371/journal.pone.0199274] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 12/12/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Resistant starch is a prebiotic metabolized by the gut bacteria. It has been shown to attenuate chronic kidney disease (CKD) progression in rats. Previous studies employed taxonomic analysis using 16S rRNA sequencing and untargeted metabolomics profiling. Here we expand these studies by metaproteomics, gaining new insight into the host-microbiome interaction. METHODS Differences between cecum contents in CKD rats fed a diet containing resistant starch with those fed a diet containing digestible starch were examined by comparative metaproteomics analysis. Taxonomic information was obtained using unique protein sequences. Our methodology results in quantitative data covering both host and bacterial proteins. RESULTS 5,834 proteins were quantified, with 947 proteins originating from the host organism. Taxonomic information derived from metaproteomics data surpassed previous 16S RNA analysis, and reached species resolutions for moderately abundant taxonomic groups. In particular, the Ruminococcaceae family becomes well resolved-with butyrate producers and amylolytic species such as R. bromii clearly visible and significantly higher while fibrolytic species such as R. flavefaciens are significantly lower with resistant starch feeding. The observed changes in protein patterns are consistent with fiber-associated improvement in CKD phenotype. Several known host CKD-associated proteins and biomarkers of impaired kidney function were significantly reduced with resistant starch supplementation. Data are available via ProteomeXchange with identifier PXD008845. CONCLUSIONS Metaproteomics analysis of cecum contents of CKD rats with and without resistant starch supplementation reveals changes within gut microbiota at unprecedented resolution, providing both functional and taxonomic information. Proteins and organisms differentially abundant with RS supplementation point toward a shift from mucin degraders to butyrate producers.
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Affiliation(s)
- Boris L Zybailov
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Galina V Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Yasir Rahmatallah
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Dmitri S Andreyev
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Taylor McElroy
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Oleg Karaduta
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Lisa Orr
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Proteomics Core Facility, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Proteomics Core Facility, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Ricky D Edmondson
- Proteomics Core Facility, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Dorothy A Kieffer
- Department of Nutrition, University of California, Davis, CA, United States of America
| | - R J Martin
- Department of Nutrition, University of California, Davis, CA, United States of America
| | - Sean H Adams
- Arkansas Children's Nutrition Center and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Nosratola D Vaziri
- Division of Nephrology, University of California, Irvine, CA, United States of America
| | - John M Arthur
- Division of Nephrology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
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40
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Byrum S, Loughran AJ, Beenken KE, Orr LM, Storey AJ, Mackintosh SG, Edmondson RD, Tackett AJ, Smeltzer MS. Label-Free Proteomic Approach to Characterize Protease-Dependent and -Independent Effects of sarA Inactivation on the Staphylococcus aureus Exoproteome. J Proteome Res 2018; 17:3384-3395. [PMID: 30209945 PMCID: PMC6209314 DOI: 10.1021/acs.jproteome.8b00288] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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] [Indexed: 01/04/2023]
Abstract
The staphylococcal accessory regulator A ( sarA) impacts the extracellular accumulation of Staphylococcus aureus virulence factors at the level of intracellular production and extracellular protease-mediated degradation. We previously used a proteomics approach that measures protein abundance of all proteoforms to demonstrate that mutation of sarA results in increased levels of extracellular proteases and assesses the impact of this on the accumulation of S. aureus exoproteins. Our previous approach was limited as it did not take into account that large, stable proteolytic products from a given protein could result in false negatives when quantified by total proteoforms. Here, our goal was to use an expanded proteomics approach utilizing a dual quantitative method for measuring abundance at both the total proteoform and full-length exoprotein levels to alleviate these false negatives and thereby provide for characterization of protease-dependent and -independent effects of sarA mutation on the S. aureus exoproteome. Proteins present in conditioned medium from overnight, stationary phase cultures of the USA300 strain LAC, an isogenic sarA mutant, and a sarA mutant unable to produce any of the known extracellular proteases ( sarA/protease) were resolved using one-dimensional gel electrophoresis. Quantitative proteomic comparisons of sarA versus sarA/protease mutants identified proteins that were cleaved in a protease-dependent manner owing to mutation of sarA, and comparisons of sarA/protease mutant versus the LAC parent strain identified proteins in which abundance was altered in a sarA mutant in a protease-independent manner. Furthermore, the proteins uniquely identified by the full-length data analysis approach eliminated false negatives observed in the total proteoform analysis. This expanded approach provided for a more comprehensive analysis of the impact of mutating sarA on the S. aureus exoproteome.
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Affiliation(s)
- Stephanie
D. Byrum
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States,Arkansas
Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas 72202, United States
| | - Allister J. Loughran
- Department
of Microbiology and Immunology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Karen E. Beenken
- Department
of Microbiology and Immunology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Lisa M. Orr
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Aaron J. Storey
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Samuel G. Mackintosh
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Ricky D. Edmondson
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Alan J. Tackett
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States,Arkansas
Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas 72202, United States,E-mail:
| | - Mark S. Smeltzer
- Department
of Microbiology and Immunology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States,E-mail: , Phone: (501) 686-7958
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Zhang X, Zhang S, Liu X, Wang Y, Chang J, Zhang X, Mackintosh SG, Tackett AJ, He Y, Lv D, Laberge RM, Campisi J, Wang J, Zheng G, Zhou D. Oxidation resistance 1 is a novel senolytic target. Aging Cell 2018; 17:e12780. [PMID: 29766639 PMCID: PMC6052462 DOI: 10.1111/acel.12780] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [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] [Accepted: 04/01/2018] [Indexed: 01/02/2023] Open
Abstract
The selective depletion of senescent cells (SCs) by small molecules, termed senolytic agents, is a promising therapeutic approach for treating age-related diseases and chemotherapy- and radiotherapy-induced side effects. Piperlongumine (PL) was recently identified as a novel senolytic agent. However, its mechanism of action and molecular targets in SCs was unknown and thus was investigated. Specifically, we used a PL-based chemical probe to pull-down PL-binding proteins from live cells and then mass spectrometry-based proteomic analysis to identify potential molecular targets of PL in SCs. One prominent target was oxidation resistance 1 (OXR1), an important antioxidant protein that regulates the expression of a variety of antioxidant enzymes. We found that OXR1 was upregulated in senescent human WI38 fibroblasts. PL bound to OXR1 directly and induced its degradation through the ubiquitin-proteasome system in an SC-specific manner. The knockdown of OXR1 expression by RNA interference significantly increased the production of reactive oxygen species in SCs in conjunction with the downregulation of antioxidant enzymes such as heme oxygenase 1, glutathione peroxidase 2, and catalase, but these effects were much less significant when OXR1 was knocked down in non-SCs. More importantly, knocking down OXR1 selectively induced apoptosis in SCs and sensitized the cells to oxidative stress caused by hydrogen peroxide. These findings provide new insights into the mechanism by which SCs are highly resistant to oxidative stress and suggest that OXR1 is a novel senolytic target that can be further exploited for the development of new senolytic agents.
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Affiliation(s)
- Xin Zhang
- Department of Pharmaceutical Sciences; College of Pharmacy; University of Arkansas for Medical Sciences; Little Rock Arkansas
| | - Suping Zhang
- Department of Pharmaceutical Sciences; College of Pharmacy; University of Arkansas for Medical Sciences; Little Rock Arkansas
- Hematology Center of Cyrus Tang Medical Institute; Collaborative Innovation Center of Hematology; Soochow University School of Medicine; Suzhou China
| | - Xingui Liu
- Department of Pharmaceutical Sciences; College of Pharmacy; University of Arkansas for Medical Sciences; Little Rock Arkansas
| | - Yingying Wang
- Department of Pharmaceutical Sciences; College of Pharmacy; University of Arkansas for Medical Sciences; Little Rock Arkansas
| | - Jianhui Chang
- Department of Pharmaceutical Sciences; College of Pharmacy; University of Arkansas for Medical Sciences; Little Rock Arkansas
| | - Xuan Zhang
- Department of Pharmaceutical Sciences; College of Pharmacy; University of Arkansas for Medical Sciences; Little Rock Arkansas
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology; College of Medicine; University of Arkansas for Medical Sciences; Little Rock Arkansas
| | - Alan J. Tackett
- Department of Biochemistry and Molecular Biology; College of Medicine; University of Arkansas for Medical Sciences; Little Rock Arkansas
| | - Yonghan He
- Department of Pharmaceutical Sciences; College of Pharmacy; University of Arkansas for Medical Sciences; Little Rock Arkansas
| | - Dongwen Lv
- Department of Pharmaceutical Sciences; College of Pharmacy; University of Arkansas for Medical Sciences; Little Rock Arkansas
| | | | - Judith Campisi
- The Buck Institute for Research on Aging; Novato California
- Lawrence Berkeley National Laboratories; Berkeley California
| | - Jianrong Wang
- Hematology Center of Cyrus Tang Medical Institute; Collaborative Innovation Center of Hematology; Soochow University School of Medicine; Suzhou China
| | - Guangrong Zheng
- Department of Pharmaceutical Sciences; College of Pharmacy; University of Arkansas for Medical Sciences; Little Rock Arkansas
- Department of Medicinal Chemistry; College of Pharmacy; University of Florida; Gainesville Florida
| | - Daohong Zhou
- Department of Pharmaceutical Sciences; College of Pharmacy; University of Arkansas for Medical Sciences; Little Rock Arkansas
- Department of Pharmcodynamics; College of Pharmacy; University of Florida; Gainesville Florida
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Holthoff ER, Byrum SD, Mackintosh SG, Kelly T, Tackett AJ, Quick CM, Post SR. Vulvar squamous cell carcinoma aggressiveness is associated with differential expression of collagen and STAT1. Clin Proteomics 2017; 14:40. [PMID: 29225558 PMCID: PMC5717999 DOI: 10.1186/s12014-017-9175-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 07/11/2017] [Accepted: 11/25/2017] [Indexed: 02/08/2023] Open
Abstract
Background Vulvar squamous cell carcinoma (vSCC) is a rare but debilitating disease. One vSCC variant comprises tumor cells that grow and expand as a cohesive sheet of cells that “pushes” and compresses the associated lymphoplasmacytic (LPC) stroma. Another vSCC variant features tumor cells that grow in loose association with one another and infiltrate the associated fibromyxoid (FMX) stroma consisting mainly of extracellular matrix. Clinically, infiltrative vSCC with FMX stroma (Inf/FMX) is significantly associated with lymph node metastases and recurrence. Methods An unbiased proteomic approach was used to identify pathways involved in the development of the different vSCC variants. Proteins extracted from formalin-fixed and paraffin-embedded tissues of 10 cases of pushing vSCC with LPC stroma (Push/LPC) and eight cases of Inf/FMX were subjected to liquid chromatography-tandem mass spectrometry (LC–MS/MS). Results Analysis identified 2265 different proteins in the 18 samples of vSCC. Of these, 282 proteins were differentially expressed between vSCC variants. Of these, 45 were higher and 237 lower in Inf/FMX compared to Push/LPC tumors. Consistent with the desmoplastic morphology and increased picrosirius red staining, expression of subunits of several collagens (Col 1, 3, 6, 14) was higher in the more aggressive Inf/FMX tumors. In contrast, signal transducer and activator of transcription 1 (STAT1), an important regulator of several inflammatory pathways, was expressed at lower levels in the Inf/FMX tumors. This finding was confirmed by immunohistochemistry using an antibody to STAT1. Informatics analysis of the differing profiles identified differences in pathways associated with integrin signaling and inflammation mediated by chemokines and cytokines. Conclusions Comparing the proteomic profiles of vSCC morphologic variants indicates that increased expression of collagen subunits and decreased expression of STAT1 are associated with a more aggressive tumor variant, defined by increased incidence of nodal metastases and tumor recurrence. Informatic analyses further identify that both alterations in cell interaction with matrix and immune function differ with tumor aggressiveness. Identification of these pathways provides a molecular basis for understanding aggressiveness of vSCC. Electronic supplementary material The online version of this article (10.1186/s12014-017-9175-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emily R Holthoff
- Department of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Slot 845, Little Rock, AR 72205 USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Slot 845, Little Rock, AR 72205 USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Slot 845, Little Rock, AR 72205 USA
| | - Thomas Kelly
- Department of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Slot 845, Little Rock, AR 72205 USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Slot 845, Little Rock, AR 72205 USA
| | - Charles M Quick
- Department of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Slot 845, Little Rock, AR 72205 USA
| | - Steven R Post
- Department of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Slot 845, Little Rock, AR 72205 USA
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Shields BD, Mahmoud F, Taylor EM, Byrum SD, Sengupta D, Koss B, Baldini G, Ransom S, Cline K, Mackintosh SG, Edmondson RD, Shalin S, Tackett AJ. Indicators of responsiveness to immune checkpoint inhibitors. Sci Rep 2017; 7:807. [PMID: 28400597 PMCID: PMC5429745 DOI: 10.1038/s41598-017-01000-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/20/2017] [Indexed: 01/25/2023] Open
Abstract
Modulation of the immune system can produce anti-tumor responses in various cancer types, including melanoma. Recently, immune checkpoint inhibitors (ICI), in single agent and combination regimens, have produced durable and long-lasting clinical responses in a subset of metastatic melanoma patients. These monoclonal antibodies, developed against CTLA-4 and PD-1, block immune-inhibitory receptors on activated T-cells, amplifying the immune response. However, even when using anti-CTLA-4 and anti-PD-1 in combination, approximately half of patients exhibit innate resistance and suffer from disease progression. Currently, it is impossible to predict therapeutic response. Here, we report the first proteomic and histone epigenetic analysis of patient metastatic melanoma tumors taken prior to checkpoint blockade, which revealed biological signatures that can stratify patients as responders or non-responders. Furthermore, our findings provide evidence of mesenchymal transition, a known mechanism of immune-escape, in non-responding melanoma tumors. We identified elevated histone H3 lysine (27) trimethylation (H3K27me3), decreased E-cadherin, and other protein features indicating a more mesenchymal phenotype in non-responding tumors. Our results have implications for checkpoint inhibitor therapy as patient specific responsiveness can be predicted through readily assayable proteins and histone epigenetic marks, and pathways activated in non-responders have been identified for therapeutic development to enhance responsiveness.
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Affiliation(s)
- Bradley D Shields
- Departments of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Fade Mahmoud
- Departments of Medicine, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Erin M Taylor
- Departments of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Stephanie D Byrum
- Departments of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Deepanwita Sengupta
- Departments of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Brian Koss
- Departments of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Giulia Baldini
- Departments of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Seth Ransom
- Departments of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Kyle Cline
- Departments of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Samuel G Mackintosh
- Departments of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Ricky D Edmondson
- Departments of Medicine, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Sara Shalin
- Departments of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA
| | - Alan J Tackett
- Departments of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA.
- Departments of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas, 72205, USA.
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44
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Byrum SD, Burdine MS, Orr L, Mackintosh SG, Authier S, Pouliot M, Hauer-Jensen M, Tackett AJ. Time- and radiation-dose dependent changes in the plasma proteome after total body irradiation of non-human primates: Implications for biomarker selection. PLoS One 2017; 12:e0174771. [PMID: 28350824 PMCID: PMC5370149 DOI: 10.1371/journal.pone.0174771] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/15/2017] [Indexed: 01/28/2023] Open
Abstract
Acute radiation syndrome (ARS) is a complex multi-organ disease resulting from total body exposure to high doses of radiation. Individuals can be exposed to total body irradiation (TBI) in a number of ways, including terrorist radiological weapons or nuclear accidents. In order to determine whether an individual has been exposed to high doses of radiation and needs countermeasure treatment, robust biomarkers are needed to estimate radiation exposure from biospecimens such as blood or urine. In order to identity such candidate biomarkers of radiation exposure, high-resolution proteomics was used to analyze plasma from non-human primates following whole body irradiation (Co-60 at 6.7 Gy and 7.4 Gy) with a twelve day observation period. A total of 663 proteins were evaluated from the plasma proteome analysis. A panel of plasma proteins with characteristic time- and dose-dependent changes was identified. In addition to the plasma proteomics study reported here, we recently identified candidate biomarkers using urine from these same non-human primates. From the proteomic analysis of both plasma and urine, we identified ten overlapping proteins that significantly differentiate both time and dose variables. These shared plasma and urine proteins represent optimal candidate biomarkers of radiation exposure.
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Affiliation(s)
- Stephanie D. Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Marie S. Burdine
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Lisa Orr
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | | | | | - Martin Hauer-Jensen
- Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Alan J. Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
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45
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Hartman JH, Miller GP, Caro AA, Byrum SD, Orr LM, Mackintosh SG, Tackett AJ, MacMillan-Crow LA, Hallberg LM, Ameredes BT, Boysen G. 1,3-Butadiene-induced mitochondrial dysfunction is correlated with mitochondrial CYP2E1 activity in Collaborative Cross mice. Toxicology 2017; 378:114-124. [PMID: 28082109 DOI: 10.1016/j.tox.2017.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/16/2016] [Accepted: 01/04/2017] [Indexed: 01/04/2023]
Abstract
Cytochrome P450 2E1 (CYP2E1) metabolizes low molecular weight hydrophobic compounds, including 1,3-butadiene, which is converted by CYP2E1 to electrophilic epoxide metabolites that covalently modify cellular proteins and DNA. Previous CYP2E1 studies have mainly focused on the enzyme localized in the endoplasmic reticulum (erCYP2E1); however, active CYP2E1 has also been found in mitochondria (mtCYP2E1) and the distribution of CYP2E1 between organelles can influence an individual's response to exposure. Relatively few studies have focused on the contribution of mtCYP2E1 to activation of chemical toxicants. We hypothesized that CYP2E1 bioactivation of 1,3-butadiene within mitochondria adversely affects mitochondrial respiratory complexes I-IV. A population of Collaborative Cross mice was exposed to air (control) or 200ppm 1,3-butadiene. Subcellular fractions (mitochondria, DNA, and microsomes) were collected from frozen livers and CYP2E1 activity was measured in microsomes and mitochondria. Individual activities of mitochondrial respiratory complexes I-IV were measured using in vitro assays and purified mitochondrial fractions. In air- and 1,3-butadiene-exposed mouse samples, mtDNA copy numbers were assessed by RT-PCR, and mtDNA integrity was assessed through a PCR-based assay. No significant changes in mtDNA copy number or integrity were observed; however, there was a decrease in overall activity of mitochondrial respiratory complexes I, II, and IV after 1,3-butadiene exposure. Additionally, higher mtCYP2E1 (but not erCYP2E1) activity was correlated with decreased mitochondrial respiratory complex activity (in complexes I-IV) in the 1,3-butadiene-exposed (not control) animals. Together, these results represent the first in vivo link between mitochondrial CYP2E1 activity and mitochondrial toxicity.
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Affiliation(s)
- Jessica H Hartman
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Grover P Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
| | - Andres A Caro
- Department of Chemistry, Hendrix College, Conway, AR, United States
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Lisa M Orr
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Lee Ann MacMillan-Crow
- Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Lance M Hallberg
- Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX, United States; Sealy Center for Environmental Health and Medicine, University of Texas Medical Branch, Galveston, TX, United States
| | - Bill T Ameredes
- Sealy Center for Environmental Health and Medicine, University of Texas Medical Branch, Galveston, TX, United States; Division of Pulmonary, Critical Care, and Sleep Medicine, and Department of Pharmacology and Toxicology, United States
| | - Gunnar Boysen
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States; The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
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46
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Ayyadevara S, Balasubramaniam M, Suri P, Mackintosh SG, Tackett AJ, Sullivan DH, Shmookler Reis RJ, Dennis RA. Proteins that accumulate with age in human skeletal-muscle aggregates contribute to declines in muscle mass and function in Caenorhabditis elegans. Aging (Albany NY) 2016; 8:3486-3497. [PMID: 27992858 PMCID: PMC5270681 DOI: 10.18632/aging.101141] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/03/2016] [Indexed: 06/06/2023]
Abstract
Protein aggregation increases with age in normal tissues, and with pathology and age in Alzheimer's hippocampus and mouse cardiac muscle. We now ask whether human skeletal muscle accumulates aggregates with age. Detergent-insoluble protein aggregates were isolated from vastus lateralis biopsies from 5 young (23–27 years of age) and 5 older (64-80 years) adults. Aggregates, quantified after gel electrophoresis, contain 2.1-fold more protein (P<0.0001) when isolated from older subjects relative to young. Of 515 proteins identified by liquid chromatography coupled to tandem mass spectrometry, 56 (11%) were significantly more abundant in older muscle, while 21 (4%) were depleted with age (each P<0.05). Orthologs to seven of these proteins were then targeted in C. elegans by RNA interference. Six of the seven knockdown treatments decreased protein aggregation (range 6-45%, P<0.01 to <0.0001) and increased muscle mass (range 1.5- to 1.85-fold, P<0.01 to <0.0001) in aged nematodes, and rescued mobility (range 1.4 to 1.65-fold, P≤0.0005 each) in a nematode amyloidopathy model. We conclude that specific aggregate proteins, discovered as differentially abundant in aging human muscle, have orthologs that contribute functionally to aggregation and age-associated muscle loss in nematodes, and thus can be considered potential drug targets for sarcopenia in humans.
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Affiliation(s)
- Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Meenakshisundaram Balasubramaniam
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Pooja Suri
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Samuel G. Mackintosh
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alan J. Tackett
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Dennis H. Sullivan
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Geriatric Research, Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Robert J. Shmookler Reis
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Geriatric Research, Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Richard A. Dennis
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Geriatric Research, Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
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47
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Blair LP, Liu Z, Labitigan RLD, Wu L, Zheng D, Xia Z, Pearson EL, Nazeer FI, Cao J, Lang SM, Rines RJ, Mackintosh SG, Moore CL, Li W, Tian B, Tackett AJ, Yan Q. KDM5 lysine demethylases are involved in maintenance of 3'UTR length. Sci Adv 2016; 2:e1501662. [PMID: 28138513 PMCID: PMC5262454 DOI: 10.1126/sciadv.1501662] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 10/20/2016] [Indexed: 06/06/2023]
Abstract
The complexity by which cells regulate gene and protein expression is multifaceted and intricate. Regulation of 3' untranslated region (UTR) processing of mRNA has been shown to play a critical role in development and disease. However, the process by which cells select alternative mRNA forms is not well understood. We discovered that the Saccharomyces cerevisiae lysine demethylase, Jhd2 (also known as KDM5), recruits 3'UTR processing machinery and promotes alteration of 3'UTR length for some genes in a demethylase-dependent manner. Interaction of Jhd2 with both chromatin and RNA suggests that Jhd2 affects selection of polyadenylation sites through a transcription-coupled mechanism. Furthermore, its mammalian homolog KDM5B (also known as JARID1B or PLU1), but not KDM5A (also known as JARID1A or RBP2), promotes shortening of CCND1 transcript in breast cancer cells. Consistent with these results, KDM5B expression correlates with shortened CCND1 in human breast tumor tissues. In contrast, both KDM5A and KDM5B are involved in the lengthening of DICER1. Our findings suggest both a novel role for this family of demethylases and a novel targetable mechanism for 3'UTR processing.
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Affiliation(s)
- Lauren P. Blair
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zongzhi Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | | | - Lizhen Wu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Zheng Xia
- Division of Biostatistics, Dan L Duncan Comprehensive Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erica L. Pearson
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Fathima I. Nazeer
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Jian Cao
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sabine M. Lang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rachel J. Rines
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72032, USA
| | - Claire L. Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Wei Li
- Division of Biostatistics, Dan L Duncan Comprehensive Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Alan J. Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72032, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
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48
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Fujiwara T, Ye S, Castro-Gomes T, Winchell CG, Andrews NW, Voth DE, Varughese KI, Mackintosh SG, Feng Y, Pavlos N, Nakamura T, Manolagas SC, Zhao H. PLEKHM1/DEF8/RAB7 complex regulates lysosome positioning and bone homeostasis. JCI Insight 2016; 1:e86330. [PMID: 27777970 DOI: 10.1172/jci.insight.86330] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Mutations of the Plekhm1 gene in humans and rats cause osteopetrosis, an inherited bone disease characterized by diminished bone resorption by osteoclasts. PLEKHM1 binds to RAB7 and is critical for lysosome trafficking. However, the molecular mechanisms by which PLEKHM1 regulates lysosomal pathways remain unknown. Here, we generated germline and conditional Plekhm1-deficient mice. These mice displayed no overt abnormalities in major organs, except for an increase in trabecular bone mass. Furthermore, loss of PLEKHM1 abrogated the peripheral distribution of lysosomes and bone resorption in osteoclasts. Mechanistically, we indicated that DEF8 interacts with PLEKHM1 and promotes its binding to RAB7, whereas the binding of FAM98A and NDEL1 with PLEKHM1 connects lysosomes to microtubules. Importantly, suppression of these proteins results in lysosome positioning and bone resorption defects similar to those of Plekhm1-null osteoclasts. Thus, PLHKEM1, DEF8, FAM98A, and NDEL1 constitute a molecular complex that regulates lysosome positioning and secretion through RAB7.
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Affiliation(s)
- Toshifumi Fujiwara
- Center for Osteoporosis and Metabolic Bone Diseases, Division of Endocrinology and Metabolism, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Shiqiao Ye
- Center for Osteoporosis and Metabolic Bone Diseases, Division of Endocrinology and Metabolism, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Thiago Castro-Gomes
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | | | - Norma W Andrews
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | | | | | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Yunfeng Feng
- Department of Pathology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Nathan Pavlos
- Center for Orthopedic Research, Dentistry and Health Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Takashi Nakamura
- Department of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University, Tokyo, Japan
| | - Stavros C Manolagas
- Center for Osteoporosis and Metabolic Bone Diseases, Division of Endocrinology and Metabolism, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Haibo Zhao
- Center for Osteoporosis and Metabolic Bone Diseases, Division of Endocrinology and Metabolism, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.,Department of Physiology and Biophysics, and
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49
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Ayyadevara S, Balasubramaniam M, Parcon PA, Barger SW, Griffin WST, Alla R, Tackett AJ, Mackintosh SG, Petricoin E, Zhou W, Shmookler Reis RJ. Proteins that mediate protein aggregation and cytotoxicity distinguish Alzheimer's hippocampus from normal controls. Aging Cell 2016; 15:924-39. [PMID: 27448508 PMCID: PMC5013017 DOI: 10.1111/acel.12501] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2016] [Indexed: 12/14/2022] Open
Abstract
Neurodegenerative diseases are distinguished by characteristic protein aggregates initiated by disease‐specific ‘seed’ proteins; however, roles of other co‐aggregated proteins remain largely unexplored. Compact hippocampal aggregates were purified from Alzheimer's and control‐subject pools using magnetic‐bead immunoaffinity pulldowns. Their components were fractionated by electrophoretic mobility and analyzed by high‐resolution proteomics. Although total detergent‐insoluble aggregates from Alzheimer's and controls had similar protein content, within the fractions isolated by tau or Aβ1–42 pulldown, the protein constituents of Alzheimer‐derived aggregates were more abundant, diverse, and post‐translationally modified than those from controls. Tau‐ and Aβ‐containing aggregates were distinguished by multiple components, and yet shared >90% of their protein constituents, implying similar accretion mechanisms. Alzheimer‐specific protein enrichment in tau‐containing aggregates was corroborated for individuals by three analyses. Five proteins inferred to co‐aggregate with tau were confirmed by precise in situ methods, including proximity ligation amplification that requires co‐localization within 40 nm. Nematode orthologs of 21 proteins, which showed Alzheimer‐specific enrichment in tau‐containing aggregates, were assessed for aggregation‐promoting roles in C. elegans by RNA‐interference ‘knockdown’. Fifteen knockdowns (71%) rescued paralysis of worms expressing muscle Aβ, and 12 (57%) rescued chemotaxis disrupted by neuronal Aβ expression. Proteins identified in compact human aggregates, bound by antibody to total tau, were thus shown to play causal roles in aggregation based on nematode models triggered by Aβ1–42. These observations imply shared mechanisms driving both types of aggregation, and/or aggregate‐mediated cross‐talk between tau and Aβ. Knowledge of protein components that promote protein accrual in diverse aggregate types implicates common mechanisms and identifies novel targets for drug intervention.
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Affiliation(s)
- Srinivas Ayyadevara
- McClellan Veterans Medical Center Central Arkansas Veterans Healthcare Service Little Rock AR 72205 USA
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR 72205 USA
| | - Meenakshisundaram Balasubramaniam
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR 72205 USA
- BioInformatics Program University of Arkansas for Medical Sciences and University of Arkansas at Little Rock Little Rock AR 72205 USA
| | - Paul A. Parcon
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR 72205 USA
| | - Steven W. Barger
- McClellan Veterans Medical Center Central Arkansas Veterans Healthcare Service Little Rock AR 72205 USA
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR 72205 USA
| | - W. Sue T. Griffin
- McClellan Veterans Medical Center Central Arkansas Veterans Healthcare Service Little Rock AR 72205 USA
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR 72205 USA
| | - Ramani Alla
- McClellan Veterans Medical Center Central Arkansas Veterans Healthcare Service Little Rock AR 72205 USA
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR 72205 USA
| | - Alan J. Tackett
- Department of Biochemistry & Molecular Biology University of Arkansas for Medical Sciences Little Rock AR 72205 USA
| | - Samuel G. Mackintosh
- Department of Biochemistry & Molecular Biology University of Arkansas for Medical Sciences Little Rock AR 72205 USA
| | - Emanuel Petricoin
- Center for Applied Proteomics and Molecular Medicine George Mason University Manassas VA 20110 USA
| | - Weidong Zhou
- Center for Applied Proteomics and Molecular Medicine George Mason University Manassas VA 20110 USA
| | - Robert J. Shmookler Reis
- McClellan Veterans Medical Center Central Arkansas Veterans Healthcare Service Little Rock AR 72205 USA
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR 72205 USA
- Department of Biochemistry & Molecular Biology University of Arkansas for Medical Sciences Little Rock AR 72205 USA
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50
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Byrd AK, Zybailov BL, Maddukuri L, Gao J, Marecki JC, Jaiswal M, Bell MR, Griffin WC, Reed MR, Chib S, Mackintosh SG, MacNicol AM, Baldini G, Eoff RL, Raney KD. Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress. J Biol Chem 2016; 291:18041-57. [PMID: 27369081 DOI: 10.1074/jbc.m116.718478] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [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: 01/28/2016] [Indexed: 12/13/2022] Open
Abstract
Cells engage numerous signaling pathways in response to oxidative stress that together repair macromolecular damage or direct the cell toward apoptosis. As a result of DNA damage, mitochondrial DNA or nuclear DNA has been shown to enter the cytoplasm where it binds to "DNA sensors," which in turn initiate signaling cascades. Here we report data that support a novel signaling pathway in response to oxidative stress mediated by specific guanine-rich sequences that can fold into G-quadruplex DNA (G4DNA). In response to oxidative stress, we demonstrate that sequences capable of forming G4DNA appear at increasing levels in the cytoplasm and participate in assembly of stress granules. Identified proteins that bind to endogenous G4DNA in the cytoplasm are known to modulate mRNA translation and participate in stress granule formation. Consistent with these findings, stress granule formation is known to regulate mRNA translation during oxidative stress. We propose a signaling pathway whereby cells can rapidly respond to DNA damage caused by oxidative stress. Guanine-rich sequences that are excised from damaged genomic DNA are proposed to enter the cytoplasm where they can regulate translation through stress granule formation. This newly proposed role for G4DNA provides an additional molecular explanation for why such sequences are prevalent in the human genome.
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Affiliation(s)
- Alicia K Byrd
- From the Departments of Biochemistry and Molecular Biology and
| | - Boris L Zybailov
- From the Departments of Biochemistry and Molecular Biology and the University of Arkansas at Little Rock/University of Arkansas for Medical Sciences (UALR/UAMS) Joint Graduate Program in Bioinformatics, University of Arkansas at Little Rock, Little Rock, Arkansas 72204
| | - Leena Maddukuri
- From the Departments of Biochemistry and Molecular Biology and
| | - Jun Gao
- From the Departments of Biochemistry and Molecular Biology and
| | - John C Marecki
- From the Departments of Biochemistry and Molecular Biology and
| | - Mihir Jaiswal
- the University of Arkansas at Little Rock/University of Arkansas for Medical Sciences (UALR/UAMS) Joint Graduate Program in Bioinformatics, University of Arkansas at Little Rock, Little Rock, Arkansas 72204
| | - Matthew R Bell
- From the Departments of Biochemistry and Molecular Biology and
| | | | - Megan R Reed
- From the Departments of Biochemistry and Molecular Biology and
| | - Shubeena Chib
- From the Departments of Biochemistry and Molecular Biology and
| | - Samuel G Mackintosh
- From the Departments of Biochemistry and Molecular Biology and the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and
| | - Angus M MacNicol
- the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and Neurobiology and Developmental Sciences and
| | - Giulia Baldini
- From the Departments of Biochemistry and Molecular Biology and
| | - Robert L Eoff
- From the Departments of Biochemistry and Molecular Biology and the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and
| | - Kevin D Raney
- From the Departments of Biochemistry and Molecular Biology and the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and
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