1
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Ritmeester-Loy SA, Draper IH, Bueter EC, Lautz JD, Zhang-Wong Y, Gustafson JA, Wilson AL, Lin C, Gafken PR, Jensen MC, Orentas R, Smith SEP. Differential protein-protein interactions underlie signaling mediated by the TCR and a 4-1BB domain-containing CAR. Sci Signal 2024; 17:eadd4671. [PMID: 38442200 PMCID: PMC10986860 DOI: 10.1126/scisignal.add4671] [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: 06/13/2022] [Accepted: 01/09/2024] [Indexed: 03/07/2024]
Abstract
Cells rely on activity-dependent protein-protein interactions to convey biological signals. For chimeric antigen receptor (CAR) T cells containing a 4-1BB costimulatory domain, receptor engagement is thought to stimulate the formation of protein complexes similar to those stimulated by T cell receptor (TCR)-mediated signaling, but the number and type of protein interaction-mediating binding domains differ between CARs and TCRs. Here, we performed coimmunoprecipitation mass spectrometry analysis of a second-generation, CD19-directed 4-1BB:ζ CAR (referred to as bbζCAR) and identified 128 proteins that increased their coassociation after target engagement. We compared activity-induced TCR and CAR signalosomes by quantitative multiplex coimmunoprecipitation and showed that bbζCAR engagement led to the activation of two modules of protein interactions, one similar to TCR signaling that was more weakly engaged by bbζCAR as compared with the TCR and one composed of TRAF signaling complexes that was not engaged by the TCR. Batch-to-batch and interindividual variations in production of the cytokine IL-2 correlated with differences in the magnitude of protein network activation. Future CAR T cell manufacturing protocols could measure, and eventually control, biological variation by monitoring these signalosome activation markers.
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Affiliation(s)
- Samuel A. Ritmeester-Loy
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Isabella H. Draper
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Eric C. Bueter
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Jonathan D Lautz
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Yue Zhang-Wong
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Joshua A. Gustafson
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Seattle Children’s Therapeutics, Seattle Children’s Research Institute, Seattle, WA 98101 USA
| | - Ashley L. Wilson
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Seattle Children’s Therapeutics, Seattle Children’s Research Institute, Seattle, WA 98101 USA
| | - Chenwei Lin
- Proteomics and Metabolomics Facility, Fred Hutchinson Cancer Center, Seattle, WA 98101, USA
| | - Philip R. Gafken
- Proteomics and Metabolomics Facility, Fred Hutchinson Cancer Center, Seattle, WA 98101, USA
| | - Michael C. Jensen
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Seattle Children’s Therapeutics, Seattle Children’s Research Institute, Seattle, WA 98101 USA
- Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
| | - Rimas Orentas
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
| | - Stephen E. P. Smith
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA 98101, USA
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2
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Logan BR, Fu D, Howard A, Fei M, Kou J, Little MR, Adom D, Mohamed FA, Blazar BR, Gafken PR, Paczesny S. Validated graft-specific biomarkers identify patients at risk for chronic graft-versus-host disease and death. J Clin Invest 2023; 133:e168575. [PMID: 37526081 PMCID: PMC10378149 DOI: 10.1172/jci168575] [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: 01/05/2023] [Accepted: 06/16/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUNDChronic graft-versus-host disease (cGVHD) is a serious complication of allogeneic hematopoietic cell transplantation (HCT). More accurate information regarding the risk of developing cGVHD is required. Bone marrow (BM) grafts contribute to lower cGVHD, which creates a dispute over whether risk biomarker scores should be used for peripheral blood (PB) and BM.METHODSDay 90 plasma proteomics from PB and BM recipients developing cGVHD revealed 5 risk markers that were added to 8 previous cGVHD markers to screen 982 HCT samples of 2 multicenter Blood and Marrow Transplant Clinical Trials Network (BMTCTN) cohorts. Each marker was tested for its association with cause-specific hazard ratios (HRs) of cGVHD using Cox-proportional-hazards models. We paired these clinical studies with biomarker measurements in a mouse model of cGVHD.RESULTSSpearman correlations between DKK3 and MMP3 were significant in both cohorts. In BMTCTN 0201 multivariate analyses, PB recipients with 1-log increase in CXCL9 and DKK3 were 1.3 times (95% CI: 1.1-1.4, P = 0.001) and 1.9 times (95%CI: 1.1-3.2, P = 0.019) and BM recipients with 1-log increase in CXCL10 and MMP3 were 1.3 times (95%CI: 1.0-1.6, P = 0.018 and P = 0.023) more likely to develop cGVHD. In BMTCTN 1202, PB patients with high CXCL9 and MMP3 were 1.1 times (95%CI: 1.0-1.2, P = 0.037) and 1.2 times (95%CI: 1.0-1.3, P = 0.009) more likely to develop cGVHD. PB patients with high biomarkers had increased likelihood to develop cGVHD in both cohorts (22%-32% versus 8%-12%, P = 0.002 and P < 0.001, respectively). Mice showed elevated circulating biomarkers before the signs of cGVHD.CONCLUSIONBiomarker levels at 3 months after HCT identify patients at risk for cGVHD occurrence.FUNDINGNIH grants R01CA168814, R21HL139934, P01CA158505, T32AI007313, and R01CA264921.
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Affiliation(s)
- Brent R. Logan
- Division of Biostatistics and Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Denggang Fu
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Alan Howard
- Be The Match and Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | - Mingwei Fei
- Be The Match and Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | - Jianqun Kou
- Division of Biostatistics and Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Morgan R. Little
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Djamilatou Adom
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Fathima A. Mohamed
- Department of Pediatrics, Division of Blood & Marrow Transplant & Cellular Therapy, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Bruce R. Blazar
- Department of Pediatrics, Division of Blood & Marrow Transplant & Cellular Therapy, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Philip R. Gafken
- Proteomics & Metabolomics shared resource, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
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3
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Kennedy J, Whiteaker JR, Ivey RG, Burian A, Chowdhury S, Tsai CF, Liu T, Lin C, Murillo OD, Lundeen RA, Jones LA, Gafken PR, Longton G, Rodland KD, Skates SJ, Landua J, Wang P, Lewis MT, Paulovich AG. Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma. Anal Chem 2022; 94:9540-9547. [PMID: 35767427 PMCID: PMC9280723 DOI: 10.1021/acs.analchem.1c04382] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite advances in proteomic technologies, clinical translation of plasma biomarkers remains low, partly due to a major bottleneck between the discovery of candidate biomarkers and costly clinical validation studies. Due to a dearth of multiplexable assays, generally only a few candidate biomarkers are tested, and the validation success rate is accordingly low. Previously, mass spectrometry-based approaches have been used to fill this gap but feature poor quantitative performance and were generally limited to hundreds of proteins. Here, we demonstrate the capability of an internal standard triggered-parallel reaction monitoring (IS-PRM) assay to greatly expand the numbers of candidates that can be tested with improved quantitative performance. The assay couples immunodepletion and fractionation with IS-PRM and was developed and implemented in human plasma to quantify 5176 peptides representing 1314 breast cancer biomarker candidates. Characterization of the IS-PRM assay demonstrated the precision (median % CV of 7.7%), linearity (median R2 > 0.999 over 4 orders of magnitude), and sensitivity (median LLOQ < 1 fmol, approximately) to enable rank-ordering of candidate biomarkers for validation studies. Using three plasma pools from breast cancer patients and three control pools, 893 proteins were quantified, of which 162 candidate biomarkers were verified in at least one of the cancer pools and 22 were verified in all three cancer pools. The assay greatly expands capabilities for quantification of large numbers of proteins and is well suited for prioritization of viable candidate biomarkers.
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Affiliation(s)
- Jacob
J. Kennedy
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Jeffrey R. Whiteaker
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Richard G. Ivey
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Aura Burian
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Shrabanti Chowdhury
- Department
of Genetics and Genomic Sciences and Icahn Institute for Data Science
and Genomic Technology, Icahn School of
Medicine at Mount Sinai, New York, New York 10029, United States
| | - Chia-Feng Tsai
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Tao Liu
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - ChenWei Lin
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Oscar D. Murillo
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Rachel A. Lundeen
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Lisa A. Jones
- Proteomics
and Metabolomics Shared Resources, Fred
Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Philip R. Gafken
- Proteomics
and Metabolomics Shared Resources, Fred
Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Gary Longton
- Public
Health Sciences Division, Fred Hutchinson
Cancer Research Center, Seattle, Washington 98109, United States
| | - Karin D. Rodland
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Steven J. Skates
- MGH
Biostatistics Center, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - John Landua
- Lester
and Sue Smith Breast Center, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Pei Wang
- Department
of Genetics and Genomic Sciences, Mount
Sinai Hospital, New York, New York 10065, United States
| | - Michael T. Lewis
- Lester
and Sue Smith Breast Center, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Amanda G. Paulovich
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States,Phone: 206-667-1912. . Fax: 206-667-2277
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4
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Mattos DR, Serrill JD, Gafken PR, McPhail KL, Vogel WK, Ishmael JE. Abstract 3916: Cyanobacterial natural product Sec61α inhibitors induce broad suppression of the glioma cell secretome. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3916] [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
Coibamide A is a cyclopeptide natural product with potent antiproliferative activity against cultured human cancer cells and subcutaneous U87-MG glioblastoma tumors in mice. We have recently determined that coibamide A binds to the Sec61 translocon channel at a site that is close, but not identical, to the binding site of the peptide/polyketide natural product apratoxin A. As the majority of secreted proteins in mammalian cells are trafficked through the conventional secretory pathway via the Sec61 translocon, this raised the possibility that coibamide A and apratoxin A block import and secretion of different Sec61 client proteins. In the present study, we analyzed and compared the secretome of human U87-MG glioblastoma cells in the presence and absence of both marine natural products.
U87-MG glioblastoma cells were treated with coibamide A (5 nM), apratoxin A (5 nM), or vehicle for 24 h. The growth media was then replaced with serum-free media for a further 24 h. Tryptic proteomic samples were generated from cell-free conditioned media and analyzed on a LC-coupled Orbitrap Fusion mass spectrometer. The high-resolution Orbitrap mass analyzer was used to both identify precursor ions for tandem mass (MS2) analysis in the ion trap mass analyzer and to quantitate those ions (MS1). Secreted proteins were identified from peptide–spectrum matches to the human protein database using a decoy database to assign an FDR and quantified from their MS1 ion intensities.
Comparison of mass spectrometric data against the human secretome database revealed 175 proteins in the U87-MG cell secretome that were identified with high confidence. Differences between coibamide A and apratoxin A treatment were not significant, however both Sec61 inhibitors induced significant suppression of the U87-MG secretome relative to vehicle-treated cells. Treatment with coibamide A or apratoxin A resulted in the reduction of 75% of quantifiable secretome (131 proteins). Of the remaining 44 proteins, 34 are directed to intracellular organelles or contain a motif associated with retention in the endoplasmic reticulum and 10 were not suppressed with treatment but were hypothesized to be Sec61 clients.
Malignant glioblastoma cells secrete proteins into the extracellular space and use complex intercellular signaling mechanisms for a survival advantage. Our results indicate that broad-acting inhibitors of Sec61-dependent co-translational translocation block the progression of a significant percentage of the U87-MG glioblastoma cell secretome including several proteins that have previously been detected as biomarkers in the cerebrospinal fluid, blood, or urine of brain tumor patients. Taken together, our work illustrates the feasibility of inducing a reversible suppression of numerous (undrugged) extracellular signals by targeting Sec61-dependent protein biogenesis in the secretory pathway with drug-like molecules.
Citation Format: Daphne R. Mattos, Jeffrey D. Serrill, Philip R. Gafken, Kerry L. McPhail, Walter K. Vogel, Jane E. Ishmael. Cyanobacterial natural product Sec61α inhibitors induce broad suppression of the glioma cell secretome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3916.
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5
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Robins LI, Clark A, Gafken PR, Alam S, Milici J, Hassan R, Wang C, Williams J, Meyers C. Hypochlorous Acid as a Disinfectant for High‐risk HPV: Insight into the mechanism of action. J Med Virol 2022; 94:3386-3393. [DOI: 10.1002/jmv.27716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Lori I. Robins
- Department of Physical Sciences, University of Washington Bothell, 18115 Campus Way NE BothellWA98011USA
| | - Andrew Clark
- Department of Physical Sciences, University of Washington Bothell, 18115 Campus Way NE BothellWA98011USA
| | - Philip R. Gafken
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave NSeattleWA98109USA
| | - Samina Alam
- Department of Microbiology and Immunology, Pennsylvania State College of MedicineHersheyPA17033USA
| | - Janice Milici
- Department of Microbiology and Immunology, Pennsylvania State College of MedicineHersheyPA17033USA
| | - Reem Hassan
- Department of Microbiology and Immunology, Pennsylvania State College of MedicineHersheyPA17033USA
| | - Che‐Yen Wang
- Department of Microbiology and Immunology, Pennsylvania State College of MedicineHersheyPA17033USA
| | - Jeff Williams
- Briotech Inc., 14120 NE 200th StWoodinvilleWA98072USA
| | - Craig Meyers
- Department of Microbiology and Immunology, Pennsylvania State College of MedicineHersheyPA17033USA
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6
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Robins LI, Keim EK, Robins DB, Edgar JS, Meschke JS, Gafken PR, Williams JF. Modifications of IL-6 by Hypochlorous Acids: Effects on Receptor Binding. ACS Omega 2021; 6:35593-35599. [PMID: 34984290 PMCID: PMC8717532 DOI: 10.1021/acsomega.1c05297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/03/2021] [Indexed: 05/16/2023]
Abstract
Interleukin-6 (IL-6) has been implicated in the pathogenesis of inflammatory events including those seen with COVID-19 patients. Positive clinical responses to monoclonal antibodies directed against IL-6 receptors (IL-6Rs) suggest that interference with IL-6-dependent activation of pro-inflammatory pathways offers a useful approach to therapy. We exposed IL-6 to hypochlorous acid (HOCl) in vitro at concentrations reported to develop in vivo. After HOCl treatment, binding of IL-6 to IL-6R was reduced in a dose-dependent manner using a bioassay with human cells engineered to provide a luminescence response to signal transduction upon receptor activation. Similar results followed the exposure of IL-6 to N-chlorotaurine (NCT) and hypobromous acid (HOBr), two other reactive species produced in vivo. SDS-PAGE analysis of HOCl-treated IL-6 showed little to no fragmentation or aggregation up to 1.75 mM HOCl, suggesting that the modifications induced at concentrations below 1.75 mM took place on the intact protein. Mass spectrometry of trypsin-digested fragments identified oxidative changes to two amino acid residues, methionine 161 and tryptophan 157, both of which have been implicated in receptor binding of the cytokine. Our findings suggest that exogenous HOCl and NCT might bring about beneficial effects in the treatment of COVID-19. Further studies on how HOCl and HOBr and their halogenated amine derivatives interact with IL-6 and related cytokines in vivo may open up alternative therapeutic interventions with these compounds in COVID-19 and other hyperinflammatory diseases.
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Affiliation(s)
- Lori I. Robins
- Department
of Physical Sciences, University of Washington
Bothell, 18115 Campus Way NE, Bothell, Washington 98011, United States
- . Tel.: +1(425)352-3208
| | - Erika K. Keim
- Department
of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, Washington 98195, United States
| | - Deborah B. Robins
- Issaquah
High School, 700 2nd Ave SE, Issaquah, Washington 98027, United States
| | - John S. Edgar
- Department
of Medicinal Chemistry, University of Washington, H172 Health Science Building, Seattle, Washington 98195, United States
| | - John S. Meschke
- Department
of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, Washington 98195, United States
| | - Philip R. Gafken
- Fred
Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington 98109, United States
| | - Jeffrey F. Williams
- Briotech
Inc., 14120 NE 200th
St, Woodinville, Washington 98072, United States
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7
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Esfandiari Nazzaro E, Sabei FY, Vogel WK, Nazari M, Nicholson KS, Gafken PR, Taratula O, Taratula O, Davare MA, Leid M. Discovery and Validation of a Compound to Target Ewing's Sarcoma. Pharmaceutics 2021; 13:pharmaceutics13101553. [PMID: 34683845 PMCID: PMC8538197 DOI: 10.3390/pharmaceutics13101553] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 12/28/2022] Open
Abstract
Ewing’s sarcoma, characterized by pathognomonic t (11; 22) (q24; q12) and related chromosomal ETS family translocations, is a rare aggressive cancer of bone and soft tissue. Current protocols that include cytotoxic chemotherapeutic agents effectively treat localized disease; however, these aggressive therapies may result in treatment-related morbidities including second-site cancers in survivors. Moreover, the five-year survival rate in patients with relapsed, recurrent, or metastatic disease is less than 30%, despite intensive therapy with these cytotoxic agents. By using high-throughput phenotypic screening of small molecule libraries, we identified a previously uncharacterized compound (ML111) that inhibited in vitro proliferation of six established Ewing’s sarcoma cell lines with nanomolar potency. Proteomic studies show that ML111 treatment induced prometaphase arrest followed by rapid caspase-dependent apoptotic cell death in Ewing’s sarcoma cell lines. ML111, delivered via methoxypoly(ethylene glycol)-polycaprolactone copolymer nanoparticles, induced dose-dependent inhibition of Ewing’s sarcoma tumor growth in a murine xenograft model and invoked prometaphase arrest in vivo, consistent with in vitro data. These results suggest that ML111 represents a promising new drug lead for further preclinical studies and is a potential clinical development for the treatment of Ewing’s sarcoma.
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Affiliation(s)
- Ellie Esfandiari Nazzaro
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Fahad Y. Sabei
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan 88723, Saudi Arabia
| | - Walter K. Vogel
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Mohamad Nazari
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Katelyn S. Nicholson
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Philip R. Gafken
- Proteomics & Metabolomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
| | - Olena Taratula
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Oleh Taratula
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
- Correspondence: (O.T.); (M.A.D.)
| | - Monika A. Davare
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA;
- Papé Pediatric Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Correspondence: (O.T.); (M.A.D.)
| | - Mark Leid
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
- Department of Integrative Biosciences, Oregon Health & Science University, Portland, OR 97239, USA
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8
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Finton KAK, Brusniak MY, Jones LA, Lin C, Fioré-Gartland AJ, Brock C, Gafken PR, Strong RK. ARTEMIS: A Novel Mass-Spec Platform for HLA-Restricted Self and Disease-Associated Peptide Discovery. Front Immunol 2021; 12:658372. [PMID: 33986749 PMCID: PMC8111693 DOI: 10.3389/fimmu.2021.658372] [Citation(s) in RCA: 7] [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] [Received: 01/25/2021] [Accepted: 03/30/2021] [Indexed: 11/25/2022] Open
Abstract
Conventional immunoprecipitation/mass spectroscopy identification of HLA-restricted peptides remains the purview of specializing laboratories, due to the complexity of the methodology, and requires computational post-analysis to assign peptides to individual alleles when using pan-HLA antibodies. We have addressed these limitations with ARTEMIS: a simple, robust, and flexible platform for peptide discovery across ligandomes, optionally including specific proteins-of-interest, that combines novel, secreted HLA-I discovery reagents spanning multiple alleles, optimized lentiviral transduction, and streamlined affinity-tag purification to improve upon conventional methods. This platform fills a middle ground between existing techniques: sensitive and adaptable, but easy and affordable enough to be widely employed by general laboratories. We used ARTEMIS to catalog allele-specific ligandomes from HEK293 cells for seven classical HLA alleles and compared results across replicates, against computational predictions, and against high-quality conventional datasets. We also applied ARTEMIS to identify potentially useful, novel HLA-restricted peptide targets from oncovirus oncoproteins and tumor-associated antigens.
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Affiliation(s)
- Kathryn A K Finton
- Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Mi-Youn Brusniak
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Lisa A Jones
- Proteomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Chenwei Lin
- Proteomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Andrew J Fioré-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Chance Brock
- Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Philip R Gafken
- Proteomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Roland K Strong
- Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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9
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Abstract
Genetic Code Expansion (GCE) can use TAG stop codons to guide site-specific incorporation of phosphoserine (pSer) into proteins. To eliminate prematurely truncated peptides, improve yields, and enhance the production of multiphosphorylated proteins, Release Factor 1 (RF1)-deficient expression hosts were developed, yet these grew slowly and their use was associated with extensive misincorporation of natural amino acids instead of pSer. Here, we merge a healthy RF1-deficient E. coli cell line with a high-efficiency pSer GCE translation system to produce a versatile pSer GCE platform in which only trace misincorporation of natural amino acids is detected even when five phosphoserines were introduced into one protein. Approximately 400 and 200 mg of singly and doubly phosphorylated GFP per liter of culture were obtained. Importantly, the lack of truncated protein permits expression of oligomeric proteins and the use of N-terminal solubility-enhancing proteins to aid phospho-protein expression and purification. To illustrate the enhanced utility of this system, we produce doubly phosphorylated STING (Stimulator of Interferon Genes), as well as triply phosphorylated BAD (Bcl2-associated agonist of cell death) complexed with 14-3-3, in quantity, purity, and homogeneity sufficient for structural biology applications. We anticipate that the facile access to phosphoproteins enabled by this system, which we call pSer-3.1G, will expand studies of the phospho-proteome.
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Affiliation(s)
- Phillip Zhu
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Philip R. Gafken
- Proteomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Ryan A. Mehl
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Richard B. Cooley
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
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10
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Jagannathan S, Ogata Y, Gafken PR, Tapscott SJ, Bradley RK. Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of facioscapulohumeral muscular dystrophy. eLife 2019; 8:41740. [PMID: 30644821 PMCID: PMC6349399 DOI: 10.7554/elife.41740] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 09/05/2018] [Accepted: 01/14/2019] [Indexed: 12/13/2022] Open
Abstract
DUX4 is a transcription factor whose misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). DUX4’s transcriptional activity has been extensively characterized, but the DUX4-induced proteome remains undescribed. Here, we report concurrent measurement of RNA and protein levels in DUX4-expressing cells via RNA-seq and quantitative mass spectrometry. DUX4 transcriptional targets were robustly translated, confirming the likely clinical relevance of proposed FSHD biomarkers. However, a multitude of mRNAs and proteins exhibited discordant expression changes upon DUX4 expression. Our dataset revealed unexpected proteomic, but not transcriptomic, dysregulation of diverse molecular pathways, including Golgi apparatus fragmentation, as well as extensive post-transcriptional buffering of stress-response genes. Key components of RNA degradation machineries, including UPF1, UPF3B, and XRN1, exhibited suppressed protein, but not mRNA, levels, explaining the build-up of aberrant RNAs that characterizes DUX4-expressing cells. Our results provide a resource for the FSHD community and illustrate the importance of post-transcriptional processes in DUX4-induced pathology.
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Affiliation(s)
- Sujatha Jagannathan
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Yuko Ogata
- Proteomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Philip R Gafken
- Proteomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
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11
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Blair KM, Mears KS, Taylor JA, Fero J, Jones LA, Gafken PR, Whitney JC, Salama NR. The Helicobacter pylori cell shape promoting protein Csd5 interacts with the cell wall, MurF, and the bacterial cytoskeleton. Mol Microbiol 2018; 110:114-127. [PMID: 30039535 DOI: 10.1111/mmi.14087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2018] [Indexed: 12/17/2022]
Abstract
Chronic infection with Helicobacter pylori can lead to the development of gastric ulcers and stomach cancers. The helical cell shape of H. pylori promotes stomach colonization. Screens for loss of helical shape have identified several periplasmic peptidoglycan (PG) hydrolases and non-enzymatic putative scaffolding proteins, including Csd5. Both over and under expression of the PG hydrolases perturb helical shape, but the mechanism used to coordinate and localize their enzymatic activities is not known. Using immunoprecipitation and mass spectrometry we identified Csd5 interactions with cytosolic proteins CcmA, a bactofilin required for helical shape, and MurF, a PG precursor synthase, as well as the inner membrane spanning ATP synthase. A combination of Csd5 domain deletions, point mutations, and transmembrane domain chimeras revealed that the N-terminal transmembrane domain promotes MurF, CcmA, and ATP synthase interactions, while the C-terminal SH3 domain mediates PG binding. We conclude that Csd5 promotes helical shape as part of a membrane associated, multi-protein shape complex that includes interactions with the periplasmic cell wall, a PG precursor synthesis enzyme, the bacterial cytoskeleton, and ATP synthase.
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Affiliation(s)
- Kris M Blair
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, Seattle, WA, 98109, USA.,Molecular and Cellular Biology Ph.D. Program, University of Washington, 1959 NE Pacific Street, HSB T-466, Box 357275, Seattle, WA, 98195-7275, USA
| | - Kevin S Mears
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, Seattle, WA, 98109, USA
| | - Jennifer A Taylor
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, Seattle, WA, 98109, USA.,Department of Microbiology, University of Washington, 1705 NE Pacific St., HSB K-343, Box 357735, Seattle, WA, 98195-7735, USA
| | - Jutta Fero
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, Seattle, WA, 98109, USA
| | - Lisa A Jones
- Proteomics Facility, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., DE-352, Seattle, WA, 98109-1024, USA
| | - Philip R Gafken
- Proteomics Facility, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., DE-352, Seattle, WA, 98109-1024, USA
| | - John C Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Nina R Salama
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, Seattle, WA, 98109, USA
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12
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Du J, Flynn R, Paz K, Ren HG, Ogata Y, Zhang Q, Gafken PR, Storer BE, Roy NH, Burkhardt JK, Mathews W, Tolar J, Lee SJ, Blazar BR, Paczesny S. Murine chronic graft-versus-host disease proteome profiling discovers CCL15 as a novel biomarker in patients. Blood 2018; 131:1743-1754. [PMID: 29348127 PMCID: PMC5897867 DOI: 10.1182/blood-2017-08-800623] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 08/05/2017] [Accepted: 01/11/2018] [Indexed: 12/27/2022] Open
Abstract
Improved diagnostic and treatment methods are needed for chronic graft-versus-host disease (cGVHD), the leading cause of late nonrelapse mortality (NRM) in long-term survivors of allogenic hematopoietic cell transplantation. Validated biomarkers that facilitate disease diagnosis and classification generally are lacking in cGVHD. Here, we conducted whole serum proteomics analysis of a well-established murine multiorgan system cGVHD model. We discovered 4 upregulated proteins during cGVHD that are targetable by genetic ablation or blocking antibodies, including the RAS and JUN kinase activator, CRKL, and CXCL7, CCL8, and CCL9 chemokines. Donor T cells lacking CRK/CRKL prevented the generation of cGVHD, germinal center reactions, and macrophage infiltration seen with wild-type T cells. Whereas antibody blockade of CCL8 or CXCL7 was ineffective in treating cGVHD, CCL9 blockade reversed cGVHD clinical manifestations, histopathological changes, and immunopathological hallmarks. Mechanistically, elevated CCL9 expression was present predominantly in vascular smooth muscle cells and uniquely seen in cGVHD mice. Plasma concentrations of CCL15, the human homolog of mouse CCL9, were elevated in a previously published cohort of 211 cGVHD patients compared with controls and associated with NRM. In a cohort of 792 patients, CCL15 measured at day +100 could not predict cGVHD occurring within the next 3 months with clinically relevant sensitivity/specificity. Our findings demonstrate for the first time the utility of preclinical proteomics screening to identify potential new targets for cGVHD and specifically CCL15 as a diagnosis marker for cGVHD. These data warrant prospective biomarker validation studies.
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Affiliation(s)
- Jing Du
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Ryan Flynn
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Katelyn Paz
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Hong-Gang Ren
- Department of Pediatrics and Immunology, Indiana University School of Medicine, Indianapolis, IN
| | | | | | | | - Barry E Storer
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA; and
| | - Nathan H Roy
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia-Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Janis K Burkhardt
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia-Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Wendy Mathews
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Stephanie J Lee
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA; and
| | - Bruce R Blazar
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Sophie Paczesny
- Department of Pediatrics and Immunology, Indiana University School of Medicine, Indianapolis, IN
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13
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Cheung RS, Castella M, Abeyta A, Gafken PR, Tucker N, Taniguchi T. Ubiquitination-Linked Phosphorylation of the FANCI S/TQ Cluster Contributes to Activation of the Fanconi Anemia I/D2 Complex. Cell Rep 2018. [PMID: 28636932 DOI: 10.1016/j.celrep.2017.05.081] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Repair of interstrand crosslinks by the Fanconi anemia (FA) pathway requires both monoubiquitination and de-ubiquitination of the FANCI/FANCD2 (FANCI/D2) complex. In the standing model, the phosphorylation of six sites in the FANCI S/TQ cluster domain occurs upstream of, and promotes, FANCI/D2 monoubiquitination. We generated phospho-specific antibodies against three different S/TQ cluster sites (serines 556, 559, and 565) on human FANCI and found that, in contrast to the standing model, distinct FANCI sites were phosphorylated either predominantly upstream (ubiquitination independent; serine 556) or downstream (ubiquitination-linked; serines 559 and 565) of FANCI/D2 monoubiquitination. Ubiquitination-linked FANCI phosphorylation inhibited FANCD2 de-ubiquitination and bypassed the need to de-ubiquitinate FANCD2 to achieve effective interstrand crosslink repair. USP1 depletion suppressed ubiquitination-linked FANCI phosphorylation despite increasing FANCI/D2 monoubiquitination, providing an explanation of why FANCD2 de-ubiquitination is important for function of the FA pathway. Our work results in a refined model of how FANCI phosphorylation activates the FANCI/D2 complex.
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Affiliation(s)
- Ronald S Cheung
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Maria Castella
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Antonio Abeyta
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Philip R Gafken
- Proteomics Core Facility, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nyka Tucker
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Toshiyasu Taniguchi
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.
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14
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Calses PC, Dhillon KK, Tucker N, Chi Y, Huang JW, Kawasumi M, Nghiem P, Wang Y, Clurman BE, Jacquemont C, Gafken PR, Sugasawa K, Saijo M, Taniguchi T. DGCR8 Mediates Repair of UV-Induced DNA Damage Independently of RNA Processing. Cell Rep 2017; 19:162-174. [PMID: 28380355 DOI: 10.1016/j.celrep.2017.03.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/24/2016] [Accepted: 03/03/2017] [Indexed: 12/20/2022] Open
Abstract
Ultraviolet (UV) radiation is a carcinogen that generates DNA lesions. Here, we demonstrate an unexpected role for DGCR8, an RNA binding protein that canonically functions with Drosha to mediate microRNA processing, in the repair of UV-induced DNA lesions. Treatment with UV induced phosphorylation on serine 153 (S153) of DGCR8 in both human and murine cells. S153 phosphorylation was critical for cellular resistance to UV, the removal of UV-induced DNA lesions, and the recovery of RNA synthesis after UV exposure but not for microRNA expression. The RNA-binding and Drosha-binding activities of DGCR8 were not critical for UV resistance. DGCR8 depletion was epistatic to defects in XPA, CSA, and CSB for UV sensitivity. DGCR8 physically interacted with CSB and RNA polymerase II. JNKs were involved in the UV-induced S153 phosphorylation. These findings suggest that UV-induced S153 phosphorylation mediates transcription-coupled nucleotide excision repair of UV-induced DNA lesions in a manner independent of microRNA processing.
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Affiliation(s)
- Philamer C Calses
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacific, HSB T-466, Seattle, WA 98195-7275, USA
| | - Kiranjit K Dhillon
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Nyka Tucker
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Yong Chi
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Jen-Wei Huang
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacific, HSB T-466, Seattle, WA 98195-7275, USA
| | - Masaoki Kawasumi
- Division of Dermatology, Department of Medicine, University of Washington, 850 Republican St., Seattle, WA 98109-4714, USA
| | - Paul Nghiem
- Division of Dermatology, Department of Medicine, University of Washington, 850 Republican St., Seattle, WA 98109-4714, USA
| | - Yemin Wang
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Bruce E Clurman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Celine Jacquemont
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Philip R Gafken
- Proteomics Core Facility, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., DE-352, Seattle, WA 98109-1024, USA
| | - Kaoru Sugasawa
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Masafumi Saijo
- Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan
| | - Toshiyasu Taniguchi
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
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15
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Liu X, Yue Z, Yu J, Daguindau E, Kushekhar K, Zhang Q, Ogata Y, Gafken PR, Inamoto Y, Gracon A, Wilkes DS, Hansen JA, Lee SJ, Chen JY, Paczesny S. Proteomic Characterization Reveals That MMP-3 Correlates With Bronchiolitis Obliterans Syndrome Following Allogeneic Hematopoietic Cell and Lung Transplantation. Am J Transplant 2016; 16:2342-51. [PMID: 26887344 PMCID: PMC4956556 DOI: 10.1111/ajt.13750] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 10/02/2015] [Revised: 02/03/2016] [Accepted: 02/05/2016] [Indexed: 01/25/2023]
Abstract
Improved diagnostic methods are needed for bronchiolitis obliterans syndrome (BOS), a serious complication after allogeneic hematopoietic cell transplantation (HCT) and lung transplantation. For protein candidate discovery, we compared plasma pools from HCT transplantation recipients with BOS at onset (n = 12), pulmonary infection (n = 16), chronic graft-versus-host disease without pulmonary involvement (n = 15) and no chronic complications after HCT (n = 15). Pools were labeled with different tags (isobaric tags for relative and absolute quantification), and two software tools identified differentially expressed proteins (≥1.5-fold change). Candidate proteins were further selected using a six-step computational biology approach. The diagnostic value of the lead candidate, matrix metalloproteinase 3 (MMP3), was evaluated by enzyme-linked immunosorbent assay in plasma of a verification cohort (n = 112) with and without BOS following HCT (n = 76) or lung transplantation (n = 36). MMP3 plasma concentrations differed significantly between patients with and without BOS (area under the receiver operating characteristic curve 0.77). Consequently, MMP3 represents a potential noninvasive blood test for diagnosis of BOS.
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Affiliation(s)
- Xiaowen Liu
- Departement of BioHealth Informatics, Indiana University
School of Informatics and Computing, Indianapolis, IN
| | - Zongliang Yue
- Departement of BioHealth Informatics, Indiana University
School of Informatics and Computing, Indianapolis, IN
| | - Jeffrey Yu
- Department of Pediatrics, Indiana University School of
Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana
University School of Medicine, Indianapolis, IN, USA
- Department of Microbiology & Immunology, Indiana
University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Cancer Center, Indiana University
School of Medicine, Indianapolis, IN, USA
| | - Etienne Daguindau
- Department of Pediatrics, Indiana University School of
Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana
University School of Medicine, Indianapolis, IN, USA
- Department of Microbiology & Immunology, Indiana
University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Cancer Center, Indiana University
School of Medicine, Indianapolis, IN, USA
| | - Kushi Kushekhar
- Department of Pediatrics, Indiana University School of
Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana
University School of Medicine, Indianapolis, IN, USA
- Department of Microbiology & Immunology, Indiana
University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Cancer Center, Indiana University
School of Medicine, Indianapolis, IN, USA
| | - Qing Zhang
- Proteomics Shared Resource, Fred Hutchinson Cancer Research
Center, Seattle, WA, USA
| | - Yuko Ogata
- Proteomics Shared Resource, Fred Hutchinson Cancer Research
Center, Seattle, WA, USA
| | - Philip R. Gafken
- Proteomics Shared Resource, Fred Hutchinson Cancer Research
Center, Seattle, WA, USA
| | - Yoshihiro Inamoto
- Clinical Research Division, Fred Hutchinson Cancer Research
Center, Seattle, WA, USA
- Division of Hematopoietic Stem Cell Transplantation,
National Cancer Center Hospital, Tokyo, Japan
| | - Adam Gracon
- Pulmonary Division, Indiana University School of Medicine,
Indianapolis, IN, USA
| | - David S. Wilkes
- Pulmonary Division, Indiana University School of Medicine,
Indianapolis, IN, USA
| | - John A. Hansen
- Clinical Research Division, Fred Hutchinson Cancer Research
Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA,
USA
| | - Stephanie J. Lee
- Clinical Research Division, Fred Hutchinson Cancer Research
Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA,
USA
| | - Jake Y. Chen
- Departement of BioHealth Informatics, Indiana University
School of Informatics and Computing, Indianapolis, IN
| | - Sophie Paczesny
- Department of Pediatrics, Indiana University School of
Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana
University School of Medicine, Indianapolis, IN, USA
- Department of Microbiology & Immunology, Indiana
University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Cancer Center, Indiana University
School of Medicine, Indianapolis, IN, USA
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16
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Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE. Proteomics-driven Antigen Discovery for Development of Vaccines Against Gonorrhea. Mol Cell Proteomics 2016; 15:2338-55. [PMID: 27141096 PMCID: PMC4937508 DOI: 10.1074/mcp.m116.058800] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [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: 02/03/2016] [Revised: 04/25/2016] [Indexed: 12/18/2022] Open
Abstract
Expanding efforts to develop preventive gonorrhea vaccines is critical because of the dire possibility of untreatable gonococcal infections. Reverse vaccinology, which includes genome and proteome mining, has proven very successful in the discovery of vaccine candidates against many pathogenic bacteria. However, progress with this approach for a gonorrhea vaccine remains in its infancy. Accordingly, we applied a comprehensive proteomic platform-isobaric tagging for absolute quantification coupled with two-dimensional liquid chromatography and mass spectrometry-to identify potential gonococcal vaccine antigens. Our previous analyses focused on cell envelopes and naturally released membrane vesicles derived from four different Neisseria gonorrhoeae strains. Here, we extended these studies to identify cell envelope proteins of N. gonorrhoeae that are ubiquitously expressed and specifically induced by physiologically relevant environmental stimuli: oxygen availability, iron deprivation, and the presence of human serum. Together, these studies enabled the identification of numerous potential gonorrhea vaccine targets. Initial characterization of five novel vaccine candidate antigens that were ubiquitously expressed under these different growth conditions demonstrated that homologs of BamA (NGO1801), LptD (NGO1715), and TamA (NGO1956), and two uncharacterized proteins, NGO2054 and NGO2139, were surface exposed, secreted via naturally released membrane vesicles, and elicited bactericidal antibodies that cross-reacted with a panel of temporally and geographically diverse isolates. In addition, analysis of polymorphisms at the nucleotide and amino acid levels showed that these vaccine candidates are highly conserved among N. gonorrhoeae strains. Finally, depletion of BamA caused a loss of N. gonorrhoeae viability, suggesting it may be an essential target. Together, our data strongly support the use of proteomics-driven discovery of potential vaccine targets as a sound approach for identifying promising gonococcal antigens.
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Affiliation(s)
- Ryszard A Zielke
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon
| | - Igor H Wierzbicki
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon
| | - Benjamin I Baarda
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon
| | - Philip R Gafken
- §Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Olusegun O Soge
- ¶Neisseria Reference Laboratory, Department of Global Health, University of Washington, Seattle, Washington
| | - King K Holmes
- ¶Neisseria Reference Laboratory, Department of Global Health, University of Washington, Seattle, Washington; ‖Departments of Medicine and Global Health, University of Washington, Seattle, Washington
| | - Ann E Jerse
- **Department of Microbiology and Immunology, F. Edward Herbert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Magnus Unemo
- ‡‡WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Microbiology, Örebro University Hospital, Örebro, Sweden
| | - Aleksandra E Sikora
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon;
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17
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Yu J, Storer BE, Kushekhar K, Abu Zaid M, Zhang Q, Gafken PR, Ogata Y, Martin PJ, Flowers ME, Hansen JA, Arora M, Cutler C, Jagasia M, Pidala J, Hamilton BK, Chen GL, Pusic I, Lee SJ, Paczesny S. Biomarker Panel for Chronic Graft-Versus-Host Disease. J Clin Oncol 2016; 34:2583-90. [PMID: 27217465 DOI: 10.1200/jco.2015.65.9615] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE To identify diagnostic and prognostic markers of chronic graft-versus-host disease (cGVHD), the major cause of morbidity and mortality after allogeneic hematopoietic cell transplantation (HCT). PATIENTS AND METHODS Using a quantitative proteomics approach, we compared pooled plasma samples obtained at matched time points after HCT (median, 103 days) from 35 patients with cGVHD and 18 without cGVHD (data are available via ProteomeXchange with identifier PXD002762). Of 105 proteins showing at least a 1.25-fold difference in expression, 22 were selected on the basis of involvement in relevant pathways and enzyme-linked immunosorbent assay availability. Chemokine (C-X-C motif) ligand 9 (CXCL9) and suppression of tumorigenicity 2 (ST2) also were measured on the basis of previously determined associations with GVHD. Concentrations of the four lead biomarkers were measured at or after diagnosis in plasma from two independent verification cohorts (n = 391) to determine their association with cGVHD. Their prognostic ability when measured at approximately day +100 after HCT was evaluated in plasma of a second verification cohort (n = 172). RESULTS Of 24 proteins measured in the first verification cohort, nine proteins were associated with cGVHD, and only four (ST2, CXCL9, matrix metalloproteinase 3, and osteopontin) were necessary to compose a four-biomarker panel with an area under the receiver operating characteristic curve (AUC) of 0.89 and significant correlation with cGVHD diagnosis, cGVHD severity, and nonrelapse mortality. In a second verification cohort, this panel distinguished patients with cGVHD (AUC, 0.75), and finally, the panel measured at day +100 could predict cGVHD occurring within the next 3 months with an AUC of 0.67 and 0.79 without and with known clinical risk factors, respectively. CONCLUSION We conclude that the biomarker panel measured at diagnosis or day +100 after HCT may allow patient stratification according to risk of cGVHD.
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Affiliation(s)
- Jeffrey Yu
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Barry E Storer
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Kushi Kushekhar
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Mohammad Abu Zaid
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Qing Zhang
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Philip R Gafken
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Yuko Ogata
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Paul J Martin
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Mary E Flowers
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - John A Hansen
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Mukta Arora
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Corey Cutler
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Madan Jagasia
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Joseph Pidala
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Betty K Hamilton
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - George L Chen
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Iskra Pusic
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Stephanie J Lee
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO
| | - Sophie Paczesny
- Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO.
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18
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Rajkovic A, Hummels KR, Witzky A, Erickson S, Gafken PR, Whitelegge JP, Faull KF, Kearns DB, Ibba M. Translation Control of Swarming Proficiency in Bacillus subtilis by 5-Amino-pentanolylated Elongation Factor P. J Biol Chem 2016; 291:10976-85. [PMID: 27002156 DOI: 10.1074/jbc.m115.712091] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 01/02/2023] Open
Abstract
Elongation factor P (EF-P) accelerates diprolyl synthesis and requires a posttranslational modification to maintain proteostasis. Two phylogenetically distinct EF-P modification pathways have been described and are encoded in the majority of Gram-negative bacteria, but neither is present in Gram-positive bacteria. Prior work suggested that the EF-P-encoding gene (efp) primarily supports Bacillus subtilis swarming differentiation, whereas EF-P in Gram-negative bacteria has a more global housekeeping role, prompting our investigation to determine whether EF-P is modified and how it impacts gene expression in motile cells. We identified a 5-aminopentanol moiety attached to Lys(32) of B. subtilis EF-P that is required for swarming motility. A fluorescent in vivo B. subtilis reporter system identified peptide motifs whose efficient synthesis was most dependent on 5-aminopentanol EF-P. Examination of the B. subtilis genome sequence showed that these EF-P-dependent peptide motifs were represented in flagellar genes. Taken together, these data show that, in B. subtilis, a previously uncharacterized posttranslational modification of EF-P can modulate the synthesis of specific diprolyl motifs present in proteins required for swarming motility.
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Affiliation(s)
- Andrei Rajkovic
- From the Molecular, Cellular, and Developmental Biology Program and Center for RNA Biology and
| | | | | | | | - Philip R Gafken
- the Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, and
| | - Julian P Whitelegge
- the Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, and Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, California 90095
| | - Kym F Faull
- the Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, and Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, California 90095
| | - Daniel B Kearns
- the Department of Biology, Indiana University, Bloomington, Indiana 47305
| | - Michael Ibba
- From the Molecular, Cellular, and Developmental Biology Program and Center for RNA Biology and Microbiology, Ohio State University, Columbus, Ohio 43210,
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19
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Dancy BCR, Chen SW, Drechsler R, Gafken PR, Olsen CP. 13C- and 15N-Labeling Strategies Combined with Mass Spectrometry Comprehensively Quantify Phospholipid Dynamics in C. elegans. PLoS One 2015; 10:e0141850. [PMID: 26528916 PMCID: PMC4631354 DOI: 10.1371/journal.pone.0141850] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/13/2015] [Indexed: 01/08/2023] Open
Abstract
Membranes define cellular and organelle boundaries, a function that is critical to all living systems. Like other biomolecules, membrane lipids are dynamically maintained, but current methods are extremely limited for monitoring lipid dynamics in living animals. We developed novel strategies in C. elegans combining 13C and 15N stable isotopes with mass spectrometry to directly quantify the replenishment rates of the individual fatty acids and intact phospholipids of the membrane. Using multiple measurements of phospholipid dynamics, we found that the phospholipid pools are replaced rapidly and at rates nearly double the turnover measured for neutral lipid populations. In fact, our analysis shows that the majority of membrane lipids are replaced each day. Furthermore, we found that stearoyl-CoA desaturases (SCDs), critical enzymes in polyunsaturated fatty acid production, play an unexpected role in influencing the overall rates of membrane maintenance as SCD depletion affected the turnover of nearly all membrane lipids. Additionally, the compromised membrane maintenance as defined by LC-MS/MS with SCD RNAi resulted in active phospholipid remodeling that we predict is critical to alleviate the impact of reduced membrane maintenance in these animals. Not only have these combined methodologies identified new facets of the impact of SCDs on the membrane, but they also have great potential to reveal many undiscovered regulators of phospholipid metabolism.
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Affiliation(s)
- Blair C. R. Dancy
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Shaw-Wen Chen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Robin Drechsler
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Philip R. Gafken
- Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Carissa Perez Olsen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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20
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Vogel WK, Gafken PR, Leid M, Filtz TM. Kinetic analysis of BCL11B multisite phosphorylation-dephosphorylation and coupled sumoylation in primary thymocytes by multiple reaction monitoring mass spectroscopy. J Proteome Res 2014; 13:5860-8. [PMID: 25423098 PMCID: PMC4261940 DOI: 10.1021/pr5007697] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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] [Indexed: 01/08/2023]
Abstract
Transcription factors with multiple post-translational modifications (PTMs) are not uncommon, but comprehensive information on site-specific dynamics and interdependence is comparatively rare. Assessing dynamic changes in the extent of PTMs has the potential to link multiple sites both to each other and to biological effects observable on the same time scale. The transcription factor and tumor suppressor BCL11B is critical to three checkpoints in T-cell development and is a target of a T-cell receptor-mediated MAP kinase signaling. Multiple reaction monitoring (MRM) mass spectroscopy was used to assess changes in relative phosphorylation on 18 of 23 serine and threonine residues and sumoylation on one of two lysine resides in BCL11B. We have resolved the composite phosphorylation-dephosphorylation and sumoylation changes of BCL11B in response to MAP kinase activation into a complex pattern of site-specific PTM changes in primary mouse thymocytes. The site-specific resolution afforded by MRM analyses revealed four kinetic patterns of phosphorylation and one of sumoylation, including both rapid simultaneous site-specific increases and decreases at putative MAP kinase proline-directed phosphorylation sites, following stimulation. These data additionally revealed a novel spatiotemporal bisphosphorylation motif consisting of two kinetically divergent proline-directed phosphorylation sites spaced five residues apart.
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Affiliation(s)
- Walter K Vogel
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University , Corvallis, Oregon 97331, United States
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21
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Zielke RA, Gafken PR, Sikora AE. Quantitative proteomic analysis of the cell envelopes and native membrane vesicles derived from gram-negative bacteria. ACTA ACUST UNITED AC 2014; 34:1F.3.1-16. [PMID: 25082006 DOI: 10.1002/9780471729259.mc01f03s34] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Proteins localized to the cell envelope and naturally released membrane vesicles (MVs) play diverse functions in physiology and pathogenesis of Gram-negative bacteria. Study of these proteome fractions is essential for better understanding the basic physiological processes, development of vaccines, and identification of potential drug targets. This unit presents gel-free quantitative proteomic methods for comprehensive proteomic profiling of the cell envelopes and MVs. The procedure starts with the precipitation of the isolated proteome fractions to remove any potential compounds that may interfere with downstream experimental steps. Subsequently, the proteins are reduced, alkylated, and subjected to trypsin digestion. The trypsinized peptides are labeled using isobaric tagging for relative and absolute quantification (iTRAQ), and analyzed samples are pooled and subjected to rigorous prefractionations by strong cation exchange (SCX) and reversed-phase (RP) liquid chromatography (LC). Finally, the tandem mass spectrometry (MS/MS) fragmentation enables peptides identification and quantification.
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Affiliation(s)
- Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon
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22
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Zielke RA, Wierzbicki IH, Weber JV, Gafken PR, Sikora AE. Quantitative proteomics of the Neisseria gonorrhoeae cell envelope and membrane vesicles for the discovery of potential therapeutic targets. Mol Cell Proteomics 2014; 13:1299-317. [PMID: 24607996 DOI: 10.1074/mcp.m113.029538] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Neisseria gonorrhoeae (GC) is a human-specific pathogen, and the agent of a sexually transmitted disease, gonorrhea. There is a critical need for new approaches to study and treat GC infections because of the growing threat of multidrug-resistant isolates and the lack of a vaccine. Despite the implied role of the GC cell envelope and membrane vesicles in colonization and infection of human tissues and cell lines, comprehensive studies have not been undertaken to elucidate their constituents. Accordingly, in pursuit of novel molecular therapeutic targets, we have applied isobaric tagging for absolute quantification coupled with liquid chromatography and mass spectrometry for proteome quantitative analyses. Mining the proteome of cell envelopes and native membrane vesicles revealed 533 and 168 common proteins, respectively, in analyzed GC strains FA1090, F62, MS11, and 1291. A total of 22 differentially abundant proteins were discovered including previously unknown proteins. Among those proteins that displayed similar abundance in four GC strains, 34 were found in both cell envelopes and membrane vesicles fractions. Focusing on one of them, a homolog of an outer membrane protein LptD, we demonstrated that its depletion caused loss of GC viability. In addition, we selected for initial characterization six predicted outer membrane proteins with unknown function, which were identified as ubiquitous in the cell envelopes derived from examined GC isolates. These studies entitled a construction of deletion mutants and analyses of their resistance to different chemical probes. Loss of NGO1985, in particular, resulted in dramatically decreased GC viability upon treatment with detergents, polymyxin B, and chloramphenicol, suggesting that this protein functions in the maintenance of the cell envelope permeability barrier. Together, these findings underscore the concept that the cell envelope and membrane vesicles contain crucial, yet under-explored determinants of GC physiology, which may represent promising targets for designing new therapeutic interventions.
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Affiliation(s)
- Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331
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23
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Flood-Nichols SK, Kazanjian AA, Tinnemore D, Gafken PR, Ogata Y, Napolitano PG, Stallings JD, Ippolito DL. Aberrant glycosylation of plasma proteins in severe preeclampsia promotes monocyte adhesion. Reprod Sci 2014; 21:204-14. [PMID: 23757314 PMCID: PMC3879990 DOI: 10.1177/1933719113492210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Glycosylation of plasma proteins increases during pregnancy. Our objectives were to investigate an anti-inflammatory role of these proteins in normal pregnancies and determine whether aberrant protein glycosylation promotes monocyte adhesion in preeclampsia. Plasma was prospectively collected from nonpregnant controls and nulliparous patients in all 3 trimesters. Patients were divided into cohorts based on the applicable postpartum diagnosis. U937 monocytes were preconditioned with enzymatically deglycosylated plasma, and monocyte adhesion to endothelial cell monolayers was quantified by spectrophotometry. Plasma from nonpregnant controls, first trimester normotensives, and first trimester patients with mild preeclampsia inhibited monocyte-endothelial cell adhesion (P < .05), but plasma from first trimester patients with severe preeclampsia and second and third trimester normotensives did not. Deglycosylating plasma proteins significantly increased adhesion in all the cohorts. These results support a role of plasma glycoprotein interaction in monocyte-endothelial cell adhesion and could suggest a novel therapeutic target for severe preeclampsia.
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Affiliation(s)
- Shannon K. Flood-Nichols
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Madigan Army Medical Center, Tacoma, WA, USA
| | - Avedis A. Kazanjian
- Department of Clinical Investigation, Madigan Army Medical Center, Tacoma, WA, USA
| | - Deborah Tinnemore
- Department of Clinical Investigation, Madigan Army Medical Center, Tacoma, WA, USA
| | - Philip R. Gafken
- Fred Hutchinson Cancer Research Center, Proteomics Facility, Seattle, WA, USA
| | - Yuko Ogata
- Fred Hutchinson Cancer Research Center, Proteomics Facility, Seattle, WA, USA
| | - Peter G. Napolitano
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Madigan Army Medical Center, Tacoma, WA, USA
| | | | - Danielle L. Ippolito
- Department of Clinical Investigation, Madigan Army Medical Center, Tacoma, WA, USA
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24
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Jones KA, Kim PD, Patel BB, Kelsen SG, Braverman A, Swinton DJ, Gafken PR, Jones LA, Lane WS, Neveu JM, Leung HCE, Shaffer SA, Leszyk JD, Stanley BA, Fox TE, Stanley A, Hall MJ, Hampel H, South CD, de la Chapelle A, Burt RW, Jones DA, Kopelovich L, Yeung AT. Immunodepletion plasma proteomics by tripleTOF 5600 and Orbitrap elite/LTQ-Orbitrap Velos/Q exactive mass spectrometers. J Proteome Res 2013; 12:4351-65. [PMID: 24004147 DOI: 10.1021/pr400307u] [Citation(s) in RCA: 39] [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: 12/19/2022]
Abstract
Plasma proteomic experiments performed rapidly and economically using several of the latest high-resolution mass spectrometers were compared. Four quantitative hyperfractionated plasma proteomics experiments were analyzed in replicates by two AB SCIEX TripleTOF 5600 and three Thermo Scientific Orbitrap (Elite/LTQ-Orbitrap Velos/Q Exactive) instruments. Each experiment compared two iTRAQ isobaric-labeled immunodepleted plasma proteomes, provided as 30 labeled peptide fractions, and 480 LC-MS/MS runs delivered >250 GB of data in 2 months. Several analysis algorithms were compared. At 1% false discovery rate, the relative comparative findings concluded that the Thermo Scientific Q Exactive Mass Spectrometer resulted in the highest number of identified proteins and unique sequences with iTRAQ quantitation. The confidence of iTRAQ fold-change for each protein is dependent on the overall ion statistics (Mascot Protein Score) attainable by each instrument. The benchmarking also suggested how to further improve the mass spectrometry parameters and HPLC conditions. Our findings highlight the special challenges presented by the low abundance peptide ions of iTRAQ plasma proteome because the dynamic range of plasma protein abundance is uniquely high compared with cell lysates, necessitating high instrument sensitivity.
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Affiliation(s)
| | | | | | - Steven G Kelsen
- Temple University School of Medicine, Philadelphia, PA 19140
| | - Alan Braverman
- Temple University School of Medicine, Philadelphia, PA 19140
| | | | - Philip R Gafken
- Proteomics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Lisa A Jones
- Proteomics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - William S Lane
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, MA 02138
| | - John M Neveu
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, MA 02138
| | - Hon-Chiu E Leung
- Mass Spectrometry and Proteomics Core Facility, Baylor College of Medicine, Houston, TX 77030
| | - Scott A Shaffer
- Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Worcester, MA 01545
| | - John D Leszyk
- Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Worcester, MA 01545
| | - Bruce A Stanley
- Mass Spectrometry Core, Penn State College of Medicine, Hershey, PA 17033
| | - Todd E Fox
- Mass Spectrometry Core, Penn State College of Medicine, Hershey, PA 17033
| | - Anne Stanley
- Mass Spectrometry Core, Penn State College of Medicine, Hershey, PA 17033
| | | | - Heather Hampel
- Human Cancer Genetics Program, the Ohio State University, Columbus, OH 43210
| | - Christopher D South
- Human Cancer Genetics Program, the Ohio State University, Columbus, OH 43210
| | | | - Randall W Burt
- Huntsman Cancer Institute, the U. of Utah, Salt Lake City, UT 84112
| | - David A Jones
- Huntsman Cancer Institute, the U. of Utah, Salt Lake City, UT 84112
| | - Levy Kopelovich
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892
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25
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Filtz TM, Vogel WK, Gafken PR, Leid M. Discovery of a bis‐phosphokinetic motif in a regulatory region of the transcription factor, BCL11B. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.1038.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Mark Leid
- Pharmaceutical SciencesOregon State UniversityCorvallisOR
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26
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Pan S, Chen R, Brand RE, Hawley S, Tamura Y, Gafken PR, Milless BP, Goodlett DR, Rush J, Brentnall TA. Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study. J Proteome Res 2012; 11:1937-48. [PMID: 22316387 DOI: 10.1021/pr201117w] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Biomarkers are most frequently proteins that are measured in the blood. Their development largely relies on antibody creation to test the protein candidate performance in blood samples of diseased versus nondiseased patients. The creation of such antibody assays has been a bottleneck in biomarker progress due to the cost, extensive time, and effort required to complete the task. Targeted proteomics is an emerging technology that is playing an increasingly important role to facilitate disease biomarker development. In this study, we applied a SRM-based targeted proteomics platform to directly detect candidate biomarker proteins in plasma to evaluate their clinical utility for pancreatic cancer detection. The characterization of these protein candidates used a clinically well-characterized cohort that included plasma samples from patients with pancreatic cancer, chronic pancreatitis, and healthy age-matched controls. Three of the five candidate proteins, including gelsolin, lumican, and tissue inhibitor of metalloproteinase 1, demonstrated an AUC value greater than 0.75 in distinguishing pancreatic cancer from the controls. In addition, we provide an analysis of the reproducibility, accuracy, and robustness of the SRM-based proteomics platform. This information addresses important technical issues that could aid in the adoption of the targeted proteomics platform for practical clinical utility.
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Affiliation(s)
- Sheng Pan
- Department of Medicine, University of Washington , Seattle, Washington 98195, United States.
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27
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Whiteaker JR, Lin C, Kennedy J, Hou L, Trute M, Sokal I, Yan P, Schoenherr RM, Zhao L, Voytovich UJ, Kelly-Spratt KS, Krasnoselsky A, Gafken PR, Hogan JM, Jones LA, Wang P, Amon L, Chodosh LA, Nelson PS, McIntosh MW, Kemp CJ, Paulovich AG. A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat Biotechnol 2011; 29:625-34. [PMID: 21685906 PMCID: PMC3232032 DOI: 10.1038/nbt.1900] [Citation(s) in RCA: 279] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 05/20/2011] [Indexed: 01/01/2023]
Abstract
High-throughput technologies can now identify hundreds of candidate protein biomarkers for any disease with relative ease. However, because there are no assays for the majority of proteins and de novo immunoassay development is prohibitively expensive, few candidate biomarkers are tested in clinical studies. We tested whether the analytical performance of a biomarker identification pipeline based on targeted mass spectrometry would be sufficient for data-dependent prioritization of candidate biomarkers, de novo development of assays and multiplexed biomarker verification. We used a data-dependent triage process to prioritize a subset of putative plasma biomarkers from >1,000 candidates previously identified using a mouse model of breast cancer. Eighty-eight novel quantitative assays based on selected reaction monitoring mass spectrometry were developed, multiplexed and evaluated in 80 plasma samples. Thirty-six proteins were verified as being elevated in the plasma of tumor-bearing animals. The analytical performance of this pipeline suggests that it should support the use of an analogous approach with human samples.
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28
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Morrish F, Noonan J, Perez-Olsen C, Gafken PR, Fitzgibbon M, Kelleher J, VanGilst M, Hockenbery D. Myc-dependent mitochondrial generation of acetyl-CoA contributes to fatty acid biosynthesis and histone acetylation during cell cycle entry. J Biol Chem 2011. [DOI: 10.1074/jbc.a110.141606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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29
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Holstein Sherwood CA, Gafken PR, Martin DB. Collision energy optimization of b- and y-ions for multiple reaction monitoring mass spectrometry. J Proteome Res 2010; 10:231-40. [PMID: 20968307 DOI: 10.1021/pr1004289] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multiple reaction monitoring (MRM) is a highly sensitive and increasingly popular method of targeted mass spectrometry (MS) that can be used to selectively detect and quantify peptides and their corresponding proteins of interest within biological samples. The sensitivity of MRM-MS is highly dependent upon the tuning of transition-specific parameters, especially the collision energy (CE) applied during peptide fragmentation. Currently, empirical equations for CE work best for y-type ions and are much less effective for other types of transitions, such as b-type ions and small y-type transitions across particular amide bonds, which could also be useful for MRM-MS if optimized for maximum signal transmission. In this work, we have performed a CE optimization of all transitions for 80 doubly charged peptides, the results of which were used to define separate CE equations for b-ions and y-ions, as well as for small y-type ions derived from the fragmentation of amide bonds bounded on the amino-terminal side by aspartic or glutamic acid residues (D/E-X transitions). This analysis yielded four major observations: (1) b-ions tend to require lower collision energies than y-ions for optimal fragmentation, while D/E-X transitions tend to require more; (2) CE equations predict the optimal CEs more closely when product ion m/z dependence is included, in addition to the current standard of precursor ion m/z dependence; (3) separate CE equations for y-ions, b-ions, and D/E-X transitions are more effective than the previous one-size-fits-all equations, but best results are achieved by optimizing transitions individually; and (4) while b-ions gain substantial signal from CE optimization-often increases of several-fold-they still tend to rank lower than y-ions from the same peptide. These results confirm the notion that y-ions are usually the first-choice transitions for MRM experiments but also demonstrate, for the first time, that b-ions can be viable targets as well, if the proper collision energies are used.
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30
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Morrish F, Noonan J, Perez-Olsen C, Gafken PR, Fitzgibbon M, Kelleher J, VanGilst M, Hockenbery D. Myc-dependent mitochondrial generation of acetyl-CoA contributes to fatty acid biosynthesis and histone acetylation during cell cycle entry. J Biol Chem 2010; 285:36267-74. [PMID: 20813845 DOI: 10.1074/jbc.m110.141606] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cell reprogramming from a quiescent to proliferative state requires coordinate activation of multiple -omic networks. These networks activate histones, increase cellular bioenergetics and the synthesis of macromolecules required for cell proliferation. However, mechanisms that coordinate the regulation of these interconnected networks are not fully understood. The oncogene c-Myc (Myc) activates cellular metabolism and global chromatin remodeling. Here we tested for an interconnection between Myc regulation of metabolism and acetylation of histones. Using [(13)C(6)]glucose and a combination of GC/MS and LC/ESI tandem mass spectrometry, we determined the fractional incorporation of (13)C-labeled 2-carbon fragments into the fatty acid palmitate, and acetyl-lysines at the N-terminal tail of histone H4 in myc(-/-) and myc(+/+) Rat1A fibroblasts. Our data demonstrate that Myc increases mitochondrial synthesis of acetyl-CoA, as the de novo synthesis of (13)C-labeled palmitate was increased 2-fold in Myc-expressing cells. Additionally, Myc induced a forty percent increase in (13)C-labeled acetyl-CoA on H4-K16. This is linked to the capacity of Myc to increase mitochondrial production of acetyl-CoA, as we show that mitochondria provide 50% of the acetyl groups on H4-K16. These data point to a key role for Myc in directing the interconnection of -omic networks, and in particular, epigenetic modification of proteins in response to proliferative signals.
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Affiliation(s)
- Fionnuala Morrish
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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31
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Unnikrishnan A, Gafken PR, Tsukiyama T. Dynamic changes in histone acetylation regulate origins of DNA replication. Nat Struct Mol Biol 2010; 17:430-7. [PMID: 20228802 DOI: 10.1038/nsmb.1780] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 01/25/2010] [Indexed: 12/22/2022]
Abstract
Although histone modifications have been implicated in many DNA-dependent processes, their precise role in DNA replication remains largely unknown. Here we describe an efficient single-step method to specifically purify histones located around an origin of replication from Saccharomyces cerevisiae. Using high-resolution MS, we have obtained a comprehensive view of the histone modifications surrounding the origin of replication throughout the cell cycle. We have discovered that acetylation of histone H3 and H4 is dynamically regulated around an origin of replication, at the level of multiply acetylated histones. Furthermore, we find that this acetylation is required for efficient origin activation during S phase.
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Affiliation(s)
- Ashwin Unnikrishnan
- Divison of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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32
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Zhang LJ, Liu X, Gafken PR, Kioussi C, Leid M. A chicken ovalbumin upstream promoter transcription factor I (COUP-TFI) complex represses expression of the gene encoding tumor necrosis factor alpha-induced protein 8 (TNFAIP8). J Biol Chem 2009; 284:6156-68. [PMID: 19112178 PMCID: PMC2649093 DOI: 10.1074/jbc.m807713200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 12/04/2008] [Indexed: 11/06/2022] Open
Abstract
The orphan nuclear receptor chicken ovalbumin upstream promoter transcription factor I (COUP-TFI) plays key roles in development and homeostasis. A tandem affinity purification procedure revealed that COUP-TFI associated with a number of transcriptional regulatory proteins in HeLa S3 cells, including the nuclear receptor corepressor (NCoR), TIF1beta/KAP-1, HDAC1, and the SWI/SNF family member Brahma. The proapoptotic protein DBC1 was also identified in COUP-TFI complexes. In vitro experiments revealed that COUP-TFI interacted directly with NCoR but in a manner different from that of other nuclear receptors. DBC1 stabilized the interaction between COUP-TFI and NCoR by interacting directly with both proteins. The gene encoding the anti-apoptotic protein TNFAIP8 (tumor necrosis factor alpha (TNFalpha)-induced protein 8) was identified as being repressed by COUP-TFI in a manner that required several of the component proteins of the COUP-TFI complex. Finally, our studies highlight a central role for COUP-TFI in the induction of the TNFAIP8 promoter by TNFalpha. Together, these studies identify a novel COUP-TFI complex that functions as a repressor of transcription and may play a role in the TNFalpha signaling pathways.
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Affiliation(s)
- Ling-juan Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, USA
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33
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Abstract
Protein phosphorylation is a reversible and frequently occurring posttranslational modification regulating a large number of biological functions. Understanding the role phosphorylation events play in biochemical pathways requires the detection of phosphorylated proteins and their phosphorylated amino acids. Mass spectrometry has developed as the premier method for characterizing phosphoproteins as it is sensitive to detecting phosphosites within a single protein or a complex protein mixture (phosphoproteomics). Here an overview is provided of the sample separation and mass spectrometry techniques commonly used for qualitative phosphoprotein analysis.
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Affiliation(s)
- Philip R Gafken
- Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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34
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Solan JL, Marquez-Rosado L, Sorgen PL, Thornton PJ, Gafken PR, Lampe PD. Phosphorylation at S365 is a gatekeeper event that changes the structure of Cx43 and prevents down-regulation by PKC. ACTA ACUST UNITED AC 2008; 179:1301-9. [PMID: 18086922 PMCID: PMC2140020 DOI: 10.1083/jcb.200707060] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phosphorylation at unspecified sites is known to regulate the life cycle (assembly, gating, and turnover) of the gap junction protein, Cx43. In this paper, we show that Cx43 is phosphorylated on S365 in cultured cells and heart tissue. Nuclear magnetic resonance structural studies of the C-terminal region of Cx43 with an S365D mutation indicate that it forms a different stable conformation than unphosphorylated wild-type Cx43. Immunolabeling with an antibody specific for Cx43 phosphorylated at S365 shows staining on gap junction structures in heart tissue that is lost upon hypoxia when Cx43 is no longer specifically localized to the intercalated disk. Efficient phosphorylation at S368, an important Cx43 channel regulatory event that increases during ischemia or PKC activation, depends on S365 being unphosphorylated. Thus, phosphorylation at S365 can serve a “gatekeeper” function that may represent a mechanism to protect cells from ischemia and phorbol ester-induced down-regulation of channel conductance.
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Affiliation(s)
- Joell L Solan
- Molecular Diagnostics Program and 2Proteomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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35
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Gafken PR, Doneanu CE, Bennett SE, Barofsky DF. Comparison of ESI-MS interfaces for the analysis of UV-crosslinked peptide-nucleic acid complexes. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 860:145-52. [PMID: 18042442 DOI: 10.1016/j.jchromb.2007.09.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 06/27/2007] [Accepted: 09/05/2007] [Indexed: 10/22/2022]
Abstract
In this report, the effectiveness of high performance liquid chromatography (HPLC) in conjunction with electrospray ionization mass spectrometry (ESI-MS) is examined as a tool for identifying the sites of crosslinking in a protein that has been photoreacted with a non-photolabeled oligonucleotide. ESI-MS and MALDI-MS analyses preceded by off-line microflow and nanoflow HPLC, on-line microflow HPLC/ESI, and on-line nanoflow HPLC/ESI interfaces were performed in order to determine their relative effectiveness in separating mixtures of nucleopeptides and identifying sites of crosslinking on the individual components. The characteristics of these four techniques as well as possibilities for improving the analysis of nucleopeptides by ESI-MS are compared and discussed.
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Affiliation(s)
- Philip R Gafken
- Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States
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36
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Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H, Schmidt A, Ossola R, Eng JK, Aebersold R, Martin DB. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J Proteome Res 2007; 7:96-103. [PMID: 17711323 PMCID: PMC2577160 DOI: 10.1021/pr070244j] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [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: 11/28/2022]
Abstract
Tandem mass spectrometry (MS/MS) is frequently used in the identification of peptides and proteins. Typical proteomic experiments rely on algorithms such as SEQUEST and MASCOT to compare thousands of tandem mass spectra against the theoretical fragment ion spectra of peptides in a database. The probabilities that these spectrum-to-sequence assignments are correct can be determined by statistical software such as PeptideProphet or through estimations based on reverse or decoy databases. However, many of the software applications that assign probabilities for MS/MS spectra to sequence matches were developed using training data sets from 3D ion-trap mass spectrometers. Given the variety of types of mass spectrometers that have become commercially available over the last 5 years, we sought to generate a data set of reference data covering multiple instrumentation platforms to facilitate both the refinement of existing computational approaches and the development of novel software tools. We analyzed the proteolytic peptides in a mixture of tryptic digests of 18 proteins, named the "ISB standard protein mix", using 8 different mass spectrometers. These include linear and 3D ion traps, two quadrupole time-of-flight platforms (qq-TOF), and two MALDI-TOF-TOF platforms. The resulting data set, which has been named the Standard Protein Mix Database, consists of over 1.1 million spectra in 150+ replicate runs on the mass spectrometers. The data were inspected for quality of separation and searched using SEQUEST. All data, including the native raw instrument and mzXML formats and the PeptideProphet validated peptide assignments, are available at http://regis-web.systemsbiology.net/PublicDatasets/.
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Affiliation(s)
- John Klimek
- Institute for Systems Biology, Seattle, WA 98103
| | | | | | | | - Amelia Peterson
- Fred Hutchinson Cancer Research Center Seattle WA 98109-1024
| | | | | | | | - Parag Mallick
- Cedars-Sinai Medical Center, Los Angeles, California 90048
| | - Hookeun Lee
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland
| | - Alexander Schmidt
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland
| | - Reto Ossola
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland
| | - Jimmy K. Eng
- Institute for Systems Biology, Seattle, WA 98103
- Fred Hutchinson Cancer Research Center Seattle WA 98109-1024
| | - Reudi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland
| | - Daniel B Martin
- Institute for Systems Biology, Seattle, WA 98103
- Fred Hutchinson Cancer Research Center Seattle WA 98109-1024
- Corresponding author: Institute for Systems Biology (phone) 206 732-1365 (fax) 206 732-1299 email
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37
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Sundararajan N, Mao D, Chan S, Koo TW, Su X, Sun L, Zhang J, Sung KB, Yamakawa M, Gafken PR, Randolph T, McLerran D, Feng Z, Berlin AA, Roth MB. Ultrasensitive detection and characterization of posttranslational modifications using surface-enhanced Raman spectroscopy. Anal Chem 2007; 78:3543-50. [PMID: 16737206 DOI: 10.1021/ac051525i] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Posttranslational modification (PTM) of proteins is likely to be the most common mechanism of altering the expression of genetic information. It is essential to characterize PTMs to establish a complete understanding of the activities of proteins. Here, we present a sensitive detection method using surface-enhanced Raman spectroscopy (SERS) that can detect PTMs from as little as zeptomoles of peptide. We demonstrate, using model peptides, the ability of SERS to detect a variety of protein modifications, such as acetylation, trimethylation, phosphorylation, and ubiquitination. In addition, we show the capability to obtain positional information for modifications such as trimethylation and phosphorylation using SERS and wavelet decomposition data analysis techniques. We further show that it is possible to apply SERS to detect PTMs from biological samples such as histones. We envision that this detection method might be a valuable technique that is complementary to mass spectrometry in obtaining orthogonal chemical and modification-specific information from biological samples at sensitive levels.
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Affiliation(s)
- Narayan Sundararajan
- Biomedical/Life Sciences, Digital Health Group, Intel Corporation, Santa Clara, California 95052, USA.
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38
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Abstract
Posttranslational regulation of proteins via protein phosphorylation is one of the major means of protein regulation. Phosphorylation is a very rapid and reversible method of changing the function of proteins. Detection of phosphorylated proteins and the identification of phosphorylation sites are necessary to molecularly link specific phosphorylated events with change in phosphoprotein function. Mass Spectrometry (MS) has become the methodology of choice for phosphosite identification. Here we review current approaches including sample separation and enrichment techniques (SDS-PAGE, immunoprecipitation, metal-assisted enrichment, strong cation exchange, dendrimer capture), quantitative MS analysis methods (SILAC, iTRAQ, AQUA), and the application of recently developed methods including electron transfer dissociation ionization and "top-down" proteomics to phosphoprotein analysis.
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Affiliation(s)
- Philip R Gafken
- Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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39
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Katzenellenbogen RA, Egelkrout EM, Vliet-Gregg P, Gewin LC, Gafken PR, Galloway DA. NFX1-123 and poly(A) binding proteins synergistically augment activation of telomerase in human papillomavirus type 16 E6-expressing cells. J Virol 2007; 81:3786-96. [PMID: 17267499 PMCID: PMC1866132 DOI: 10.1128/jvi.02007-06] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [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: 01/01/2023] Open
Abstract
Overcoming senescence signals in somatic cells is critical to cellular immortalization and carcinogenesis. High-risk human papillomavirus (HPV) can immortalize epithelial cells in culture through degradation of the retinoblastoma protein by HPV E7 and activation of hTERT transcription, the catalytic subunit of telomerase, by the heterodimer HPV E6/E6-associated protein (E6AP). Recent work in our laboratory identified a novel repressor of hTERT transcription, NFX1-91, which is targeted for ubiquitin-mediated degradation by HPV type 16 (HPV16) E6/E6AP. In contrast, NFX1-123, a splice variant NFX1, increased expression from an hTERT promoter that was activated by HPV16 E6/E6AP. Here, we show that HPV16 E6 bound both NFX1-91 and NFX1-123 through the common central domain of NFX1 in the absence of E6AP. NFX1-123 positively regulated hTERT expression, as its knockdown decreased hTERT mRNA levels and telomerase activity and its overexpression increased telomerase activity. We identified new protein partners of NFX1-123, including several cytoplasmic poly(A) binding proteins (PABPCs) that interacted with NFX1-123 through its N-terminal PAM2 motif, a protein domain characteristic of other PABPC protein partners. Furthermore, NFX1-123 and PABPCs together had a synergistic stimulatory effect on hTERT-regulated reporter assays. The data suggest that NFX1-123 is integral to hTERT regulation in HPV16 E6-expressing epithelial cells and that the interaction between NFX1-123 and PABPCs is critical to hTERT activity.
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Affiliation(s)
- Rachel A Katzenellenbogen
- Fred Hutchinson Cancer Research Center, and Department of Pediatrics, University of Washington, Seattle, WA 98109, USA.
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40
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Abstract
The family of myc proto-oncogenes encodes transcription factors (c-, N-, and L-Myc) that regulate cell growth and proliferation and are involved in the etiology of diverse cancers. Myc proteins are thought to function by binding and regulating specific target genes. Here we report that Myc proteins are required for the widespread maintenance of active chromatin. Disruption of N-myc in neuronal progenitors and other cell types leads to nuclear condensation accompanied by large-scale changes in histone modifications associated with chromatin inactivation, including hypoacetylation and altered methylation. These effects are largely reversed by exogenous Myc as well as by differentiation and are mimicked by the Myc antagonist Mad1. The first chromatin changes are evident within 6 h of Myc loss and lead to changes in chromatin structure. Myc widely influences chromatin in part through upregulation of the histone acetyltransferase GCN5. This study provides the first evidence for regulation of global chromatin structure by an oncoprotein and may explain the broad effects of Myc on cell behavior and tumorigenesis.
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Affiliation(s)
- Paul S Knoepfler
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Xiao-yong Zhang
- The Wistar Institute, Gene Expression and Regulation Program, Philadelphia, PA, USA
| | - Pei Feng Cheng
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Philip R Gafken
- Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven B McMahon
- The Wistar Institute, Gene Expression and Regulation Program, Philadelphia, PA, USA
| | - Robert N Eisenman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Doneanu CE, Gafken PR, Bennett SE, Barofsky DF. Mass spectrometry of UV-cross-linked protein-nucleic acid complexes: identification of amino acid residues in the single-stranded DNA-binding domain of human replication protein A. Anal Chem 2006; 76:5667-76. [PMID: 15456284 DOI: 10.1021/ac049547c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photochemical cross-linking of human replication protein A (hRPA) to oligonucleotide dT30 was performed to enable identification of amino acid sequences that reside in the DNA-binding domain. A nucleoprotein complex, with a 1:1 protein/DNA stoichiometry, was separated from unreacted enzyme and oligonucleotide by SDS-polyacrylamide gel electrophoresis and subjected to in-gel digestion with trypsin. Three cross-linked tryptic peptides (nucleopeptides) of hRPA70xdT30 (T43, T28/29, and a truncated T24/25) were isolated. Combined mass spectrometric and C-terminal proteolysis experiments showed that at least one amino acid in the segment 235-ATAFNE-240 (located in T24/25), at least one out of the two residues sequence 269-FT-270 (located in T28/29), and at least one from the sequence 383-VSDF-386 (located in T43) were involved in cross-linking. These peptides contained aromatic residues (F238, F269, and F386 respectively) that can form base-stacking interactions with the DNA and were, therefore, most likely to be involved in cross-linking. The results obtained in this study demonstrate that a combination of exhaustive proteolysis and MALDI TOF MS can localize the sites of DNA binding to very short sequences of amino acids. Data so acquired can confirm or amend information obtained from site-directed mutagenesis and X-ray crystallography.
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Affiliation(s)
- Catalin E Doneanu
- Department of Chemistry, Department of Environmental & Molecular Toxicology, and Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331 USA
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Mitchell BL, Yasui Y, Lampe JW, Gafken PR, Lampe PD. Evaluation of matrix-assisted laser desorption/ionization-time of flight mass spectrometry proteomic profiling: identification of alpha 2-HS glycoprotein B-chain as a biomarker of diet. Proteomics 2005; 5:2238-46. [PMID: 15841498 DOI: 10.1002/pmic.200401099] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [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: 11/09/2022]
Abstract
Biomarkers have the potential to impact a wide range of public health concerns, including early detection of diseases, drug discovery, and improved accuracy of monitoring effects of interventions. Given new technological developments, broad-based screening approaches will likely advance biomarker discovery at an accelerated pace. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) allows for the elucidation of individual protein masses from a complex mixture with high throughput. We have developed a method for identifying serum biomarkers using MALDI-TOF and statistical analysis. However, before applying this approach to screening of complex diseases, we evaluated the approach in a controlled dietary intervention study. In this study, MALDI-TOF spectra were generated using samples from a randomized controlled trial. During separate feeding periods, 38 participants ate a basal diet devoid of fruits and vegetables and a basal diet supplemented with cruciferous (broccoli) family vegetables. Serum samples were obtained at the end of each 7-day feeding period and treated to remove large, abundant proteins. MALDI-TOF spectra were analyzed using peak picking algorithms and logistic regression models. Our bioinformatics methods identified two significant peaks at m/z values of 2740 and 1847 that could classify participants based on diet (basal vs. cruciferous) with 76% accuracy. The 2740 m/z peak was identified as the B-chain of alpha 2-HS glycoprotein, a serum protein previously found to vary with diet and be involved in insulin resistance and immune function.
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Affiliation(s)
- Breeana L Mitchell
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, 98109, USA
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Farr CD, Gafken PR, Norbeck AD, Doneanu CE, Stapels MD, Barofsky DF, Minami M, Saugstad JA. Proteomic analysis of native metabotropic glutamate receptor 5 protein complexes reveals novel molecular constituents. J Neurochem 2004; 91:438-50. [PMID: 15447677 PMCID: PMC2747775 DOI: 10.1111/j.1471-4159.2004.02735.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We used a proteomic approach to identify novel proteins that may regulate metabotropic glutamate receptor 5 (mGluR5) responses by direct or indirect protein interactions. This approach does not rely on the heterologous expression of proteins and offers the advantage of identifying protein interactions in a native environment. The mGluR5 protein was immunoprecipitated from rat brain lysates; co-immunoprecipitating proteins were analyzed by mass spectrometry and identified peptides were matched to protein databases to determine the correlating parent proteins. This proteomic approach revealed the interaction of mGluR5 with known regulatory proteins, as well as novel proteins that reflect previously unidentified molecular constituents of the mGluR5-signaling complex. Immunoblot analysis confirmed the interaction of high confidence proteins, such as phosphofurin acidic cluster sorting protein 1, microtubule-associated protein 2a and dynamin 1, as mGluR5-interacting proteins. These studies show that a proteomic approach can be used to identify candidate interacting proteins. This approach may be particularly useful for neurobiology applications where distinct protein interactions within a signaling complex can dramatically alter the outcome of the response to neurotransmitter release, or the disruption of normal protein interactions can lead to severe neurological and psychiatric disorders.
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Affiliation(s)
- Carol D. Farr
- Robert S. Dow Neurobiology Laboratories, Legacy Research, Portland, Oregon, USA
| | - Philip R. Gafken
- Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Angela D. Norbeck
- Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Catalin E. Doneanu
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Martha D. Stapels
- Department of Chemistry, Oregon State University, Corvallis, Oregon, USA
| | - Douglas F. Barofsky
- Department of Chemistry, Oregon State University, Corvallis, Oregon, USA
- Mass Spectrometry Core Facility of the Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Manabu Minami
- Robert S. Dow Neurobiology Laboratories, Legacy Research, Portland, Oregon, USA
| | - Julie A. Saugstad
- Robert S. Dow Neurobiology Laboratories, Legacy Research, Portland, Oregon, USA
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McKittrick E, Gafken PR, Ahmad K, Henikoff S. Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc Natl Acad Sci U S A 2004; 101:1525-30. [PMID: 14732680 PMCID: PMC341768 DOI: 10.1073/pnas.0308092100] [Citation(s) in RCA: 376] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin states can be distinguished by differential covalent modifications of histones or by utilization of histone variants. Chromatin associated with transcriptionally active loci becomes enriched for histones with particular lysine modifications and accumulates the H3.3 histone variant, the substrate for replication-independent nucleosome assembly. However, studies of modifications at particular loci have not distinguished between histone variants, so the relationship among modifications, histone variants, and nucleosome assembly pathways is unclear. To address this uncertainty, we have quantified the relative abundance of H3 and H3.3 and their lysine modifications. Using a Drosophila cell line system in which H3.3 has been shown to specifically package active loci, we found that H3.3 accounts for approximately 25% of total histone 3 in bulk chromatin, enough to package essentially all actively transcribed genes. MS and antibody characterization of separated histone 3 fractions revealed that H3.3 is relatively enriched in modifications associated with transcriptional activity and deficient in dimethyl lysine-9, which is abundant in heterochromatin. To explain enrichment on alternative variants, we propose that histone modifications are tied to the alternative nucleosome assembly pathways that use primarily H3 at replication forks and H3.3 at actively transcribed genes in a replication-independent manner.
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Affiliation(s)
- Erin McKittrick
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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Smith CM, Gafken PR, Zhang Z, Gottschling DE, Smith JB, Smith DL. Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4. Anal Biochem 2003; 316:23-33. [PMID: 12694723 DOI: 10.1016/s0003-2697(03)00032-0] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.1] [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: 11/24/2022]
Abstract
Electrospray ionization mass spectrometry, a leading method for the quantification of biomolecules, is useful for the analysis of posttranslational modifications of proteins. Here we describe a mass spectrometric approach for determining levels of acetylation at individual lysine residues within the amino-terminal tail of histone H4. Because of the high density of acetylatable lysine residues within this short span of amino acids, collision-induced dissociation tandem mass spectrometry was required. In addition, it was necessary to develop an algorithm to determine the fraction of acetylation at specific lysine residues from fragment ions containing more than one lysine residue. This is the first report of direct measurement of endogeneous levels of acetylation at individual lysine residues within the amino-terminal tail of yeast histone H4 and is the first use of tandem mass spectrometry for quantification of peptides containing multiple sites of modification.
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Affiliation(s)
- Christine M Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.
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Smith CM, Haimberger ZW, Johnson CO, Wolf AJ, Gafken PR, Zhang Z, Parthun MR, Gottschling DE. Heritable chromatin structure: mapping "memory" in histones H3 and H4. Proc Natl Acad Sci U S A 2002; 99 Suppl 4:16454-61. [PMID: 12196632 PMCID: PMC139908 DOI: 10.1073/pnas.182424999] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [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: 11/18/2022] Open
Abstract
Telomeric position effect in Saccharomyces cerevisiae is a chromatin-mediated phenomenon in which telomere proximal genes are repressed (silenced) in a heritable, but reversible, fashion. Once a transcriptional state (active or silenced) is established, however, there is a strong tendency for that state to be propagated. Twenty-five years ago, H. Weintraub and colleagues suggested that such heritability could be mediated by posttranslational modification of chromatin [Weintraub, H., Flint, S. J., Leffak, I. M., Groudine, M. & Grainger, R. M. (1977) Cold Spring Harbor Symp. Quant. Biol. 42, 401-407]. To identify potential sites within the chromatin that might act as sources of "memory" for the heritable transmission, we performed a genetic screen to isolate mutant alleles of the histones H3 and H4 genes that would "lock" telomeric marker genes into a silenced state. We identified mutations in the NH(2)-terminal tail and core of both histones; most of the amino acid changes mapped adjacent to lysines that are known sites of acetylation or methylation. We developed a method using MS to quantify the level of acetylation at each lysine within the histone H4 NH(2)-terminal tail in these mutants. We discovered that each of these mutants had a dramatic reduction in the level of acetylation at lysine 12 within the histone H4 tail. We propose that this lysine serves as a "memory mark" for propagating the expression state of a telomeric gene: when it is unacetylated, silent chromatin will be inherited; when it is acetylated an active state will be inherited.
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Affiliation(s)
- Christine M Smith
- Division of Basic Sciences and Proteomics Facility, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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Abstract
DOT1 was originally identified as a gene affecting telomeric silencing in S. cerevisiae. We now find that Dot1p methylates histone H3 on lysine 79, which maps to the top and bottom of the nucleosome core. Methylation occurs only when histone H3 is assembled in chromatin. In vivo, Dot1p is solely responsible for this methylation and methylates approximately 90% of histone H3. In dot1delta cells, silencing is compromised and silencing proteins become redistributed at the expense of normally silenced loci. We suggest that methylation of histone H3 lysine 79 limits silencing to discrete loci by preventing the binding of Sir proteins elsewhere along the genome. Because Dot1p and histone H3 are conserved, similar mechanisms are likely at work in other eukaryotes.
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Affiliation(s)
- Fred van Leeuwen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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