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Mehaffey MR, Sanders JD, Holden DD, Nilsson CL, Brodbelt JS. Multistage Ultraviolet Photodissociation Mass Spectrometry To Characterize Single Amino Acid Variants of Human Mitochondrial BCAT2. Anal Chem 2018; 90:9904-9911. [PMID: 30016590 PMCID: PMC6323636 DOI: 10.1021/acs.analchem.8b02099] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Unraveling disease mechanisms requires a comprehensive understanding of how the interplay between higher-order structure and protein-ligand interactions impacts the function of a given protein. Recent advances in native mass spectrometry (MS) involving multimodal or higher-energy activation methods have allowed direct interrogation of intact protein complexes in the gas phase, allowing analysis of both composition and subunit connectivity. We report a multistage approach combining collisional activation and 193 nm ultraviolet photodissociation (UVPD) to characterize single amino acid variants of the human mitochondrial enzyme branched-chain amino acid transferase 2 (BCAT2), a protein implicated in chemotherapeutic resistance in glioblastoma tumors. Native electrospray ionization confirms that both proteins exist as homodimers. Front-end collisional activation disassembles the dimers into monomeric subunits that are further interrogated using UVPD to yield high sequence coverage of the mutated region. Additionally, holo (ligand-bound) fragment ions resulting from photodissociation reveal that the mutation causes destabilization of the interactions with a bound cofactor. This study demonstrates the unique advantages of implementing UVPD in a multistage MS approach for analyzing intact protein assemblies.
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Affiliation(s)
- M. Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - Dustin D. Holden
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - Carol L. Nilsson
- Institute of Experimental Medical Sciences, Lund University, SE-221, Lund Sweden
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Mirgorodskaya E, Karlsson NG, Sihlbom C, Larson G, Nilsson CL. Cracking the Sugar Code by Mass Spectrometry : An Invited Perspective in Honor of Dr. Catherine E. Costello, Recipient of the 2017 ASMS Distinguished Contribution Award. J Am Soc Mass Spectrom 2018; 29:1065-1074. [PMID: 29644549 PMCID: PMC6003999 DOI: 10.1007/s13361-018-1912-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
The structural study of glycans and glycoconjugates is essential to assign their roles in homeostasis, health, and disease. Once dominated by nuclear magnetic resonance spectroscopy, mass spectrometric methods have become the preferred toolbox for the determination of glycan structures at high sensitivity. The patterns of such structures in different cellular states now allow us to interpret the sugar codes in health and disease, based on structure-function relationships. Dr. Catherine E. Costello was the 2017 recipient of the American Society for Mass Spectrometry's Distinguished Contribution Award. In this Perspective article, we describe her seminal work in a historical and geographical context and review the impact of her research accomplishments in the field.8 ᅟ Graphical abstract.
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Affiliation(s)
- Ekaterina Mirgorodskaya
- Proteomics Core Facility, University of Gothenburg, Sahlgrenska Academy, Box 413, SE-405 30, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry, University of Gothenburg, Sahlgrenska Academy, Box 440, SE-405 30, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, University of Gothenburg, Sahlgrenska Academy, Box 413, SE-405 30, Gothenburg, Sweden
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, Sahlgrenska Academy, Institute of Biomedicine, SE-413 45, Gothenburg, Sweden
| | - Carol L Nilsson
- Department of Experimental Medical Science, Lund University, SE-223 62, Lund, Sweden.
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Mostovenko E, Végvári Á, Rezeli M, Lichti CF, Fenyö D, Wang Q, Lang FF, Sulman EP, Sahlin KB, Marko-Varga G, Nilsson CL. Large Scale Identification of Variant Proteins in Glioma Stem Cells. ACS Chem Neurosci 2018; 9:73-79. [PMID: 29254333 DOI: 10.1021/acschemneuro.7b00362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma (GBM), the most malignant of primary brain tumors, is a devastating and deadly disease, with a median survival of 14 months from diagnosis, despite standard regimens of radical brain tumor surgery, maximal safe radiation, and concomitant chemotherapy. GBM tumors nearly always re-emerge after initial treatment and frequently display resistance to current treatments. One theory that may explain GBM re-emergence is the existence of glioma stemlike cells (GSCs). We sought to identify variant protein features expressed in low passage GSCs derived from patient tumors. To this end, we developed a proteomic database that reflected variant and nonvariant sequences in the human proteome, and applied a novel retrograde proteomic workflow, to identify and validate the expression of 126 protein variants in 33 glioma stem cell strains. These newly identified proteins may harbor a subset of novel protein targets for future development of GBM therapy.
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Affiliation(s)
- Ekaterina Mostovenko
- Department
of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, 1217 E. Marshall St., Richmond, Virginia 23284, United States
| | - Ákos Végvári
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, SE-221 84 Lund, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, SE-221 84 Lund, Sweden
| | - Cheryl F. Lichti
- Department
of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, 1217 E. Marshall St., Richmond, Virginia 23284, United States
- Department
of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave., St.
Louis, Missouri 63110, United States
| | - David Fenyö
- Department
of Biochemistry and Molecular Pharmacology and Institute for Systems
Genetics, New York University School of Medicine, New York, New York 10016, United States
| | | | | | | | - K. Barbara Sahlin
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, SE-221 84 Lund, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, SE-221 84 Lund, Sweden
| | - Carol L. Nilsson
- Center
of Excellence in Biological and Medical Mass Spectrometry, Lund University, Klinikgatan 32, SE-221 84 Lund, Sweden
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4
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Affiliation(s)
- Carol L. Nilsson
- Department of Experimental Medical
Science, Lund University, Lund, Sweden
| | - Kathryn A. Cunningham
- Department of
Pharmacology and Toxicology,
and Center for Addiction Research, University of Texas, Galveston, Texas, United States
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Mostovenko E, Liu Y, Amirian ES, Tsavachidis S, Armstrong GN, Bondy ML, Nilsson CL. Combined Proteomic-Molecular Epidemiology Approach to Identify Precision Targets in Brain Cancer. ACS Chem Neurosci 2018; 9:80-84. [PMID: 28657708 DOI: 10.1021/acschemneuro.7b00165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Primary brain tumors are predominantly malignant gliomas. Grade IV astrocytomas (glioblastomas, GBM) are among the most deadly of all tumors; most patients will succumb to their disease within 2 years of diagnosis despite standard of care. The grim outlook for brain tumor patients indicates that novel precision therapeutic targets must be identified. Our hypothesis is that the cancer proteomes of glioma tumors may contain protein variants that are linked to the aggressive pathology of the disease. To this end, we devised a novel workflow that combined variant proteomics with molecular epidemiological mining of public cancer data sets to identify 10 previously unrecognized variants linked to the risk of death in low grade glioma or GBM. We hypothesize that a subset of the protein variants may be successfully developed in the future as novel targets for malignant gliomas.
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Affiliation(s)
- Ekaterina Mostovenko
- Department of Anatomy, Virginia Commonwealth University, 1217 E. Marshall St., Richmond, Virginia 23284 United States
| | - Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, United States
- Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, United States
| | - E. Susan Amirian
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Spiridon Tsavachidis
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Georgina N. Armstrong
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Melissa L. Bondy
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, United States
- Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Carol L. Nilsson
- Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
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Abstract
Chemotherapeutics are vital for treating brain tumors such as glioblastoma, an aggressive and prolific cancer predominantly treated with DNA alkylating agents. The efficacy of antiglioblastoma drugs, such as temozolomide, is limited by their rapid clearance and instability under normal physiological conditions. Both local and systemic polymer-based therapeutics have shown promise for treating many cancers, and as such there is a growing interest in applying polymer techniques to augment the efficacy and stability of glioblastoma chemotherapeutics. Notably, brain tumor chemotherapy presents unique challenges and will require tailored delivery systems to develop markedly improved treatments.
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Affiliation(s)
- Matthew Skinner
- Polymer
Science and Engineering Department, University of Massachusetts, 120 Governors Drive, Amherst, Massachusetts 01003, United States
| | - Sarah M. Ward
- Polymer
Science and Engineering Department, University of Massachusetts, 120 Governors Drive, Amherst, Massachusetts 01003, United States
| | - Carol L. Nilsson
- Department
of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Todd Emrick
- Polymer
Science and Engineering Department, University of Massachusetts, 120 Governors Drive, Amherst, Massachusetts 01003, United States
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Anderson LC, Håkansson M, Walse B, Nilsson CL. Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2). J Am Soc Mass Spectrom 2017; 28:1796-1804. [PMID: 28681360 PMCID: PMC5556139 DOI: 10.1007/s13361-017-1705-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/21/2017] [Accepted: 04/29/2017] [Indexed: 05/16/2023]
Abstract
Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments. The enzyme generates glutamate, which is neurotoxic. To elucidate structural coordinates that may confer altered substrate binding or activity of the variant BCAT2 T186R, a ~45 kDa protein, we applied combined ETD and CID top-down mass spectrometry in a LC-FT-ICR MS at 21 T, and X-Ray crystallography in the study of both the variant and non-variant intact proteins. The combined ETD/CID fragmentation pattern allowed for not only extensive sequence coverage but also confident localization of the amino acid variant to its position in the sequence. The crystallographic experiments confirmed the hypothesis generated by in silico structural homology modeling, that the Lys59 side-chain of BCAT2 may repulse the Arg186 in the variant protein (PDB code: 5MPR), leading to destabilization of the protein dimer and altered enzyme kinetics. Taken together, the MS and novel 3D structural data give us reason to further pursue BCAT2 T186R as a precision drug target in GBM. Graphical Abstract ᅟ.
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Affiliation(s)
- Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Carol L Nilsson
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX, 77555-1074, USA.
- Institute of Clinical Sciences-Lund, Lund University, SE-221 85, Lund, Sweden.
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8
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Kroes RA, Nilsson CL. Towards the Molecular Foundations of Glutamatergic-targeted Antidepressants. Curr Neuropharmacol 2017; 15:35-46. [PMID: 26955966 PMCID: PMC5327457 DOI: 10.2174/1570159x14666160309114740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 05/08/2015] [Accepted: 01/30/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Depression affects over 120 million individuals of all ages and is the leading cause of disability worldwide. The lack of objective diagnostic criteria, together with the heterogeneity of the depressive disorder itself, makes it challenging to develop effective therapies. The accumulation of preclinical data over the past 20 years derived from a multitude of models using many divergent approaches, has fueled the resurgence of interest in targeting glutamatergic neurotransmission for the treatment of major depression. OBJECTIVE The emergence of mechanistic studies are advancing our understanding of the molecular underpinnings of depression. While clearly far from complete and conclusive, they offer the potential to lead to the rational design of more specific therapeutic strategies and the development of safer and more effective rapid acting, long lasting antidepressants. METHODS The development of comprehensive omics-based approaches to the dysregulation of synaptic transmission and plasticity that underlies the core pathophysiology of MDD are reviewed to illustrate the fundamental elements. RESULTS This review frames the rationale for the conceptualization of depression as a "pathway disease". As such, it culminates in the call for the development of novel state-of-the-art "-omics approaches" and neurosystems biological techniques necessary to advance our understanding of spatiotemporal interactions associated with targeting glutamatergic-triggered signaling in the CNS. CONCLUSION These technologies will enable the development of novel psychiatric medications specifically targeted to impact specific, critical intracellular networks in a more focused manner and have the potential to offer new dimensions in the area of translational neuropsychiatry.
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Affiliation(s)
- Roger A. Kroes
- Naurex, Inc., 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Carol L. Nilsson
- Department of Pharmacology & Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555-1074, United States
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9
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Wang X, Zhang Y, Nilsson CL, Berven FS, Andrén PE, Carlsohn E, Horvatovich P, Malm J, Fuentes M, Végvári Á, Welinder C, Fehniger TE, Rezeli M, Edula G, Hober S, Nishimura T, Marko-Varga G. Association of chromosome 19 to lung cancer genotypes and phenotypes. Cancer Metastasis Rev 2016; 34:217-26. [PMID: 25982285 DOI: 10.1007/s10555-015-9556-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The Chromosome 19 Consortium, a part of the Chromosome-Centric Human Proteome Project (C-HPP, http://www.C-HPP.org ), is tasked with the understanding chromosome 19 functions at the gene and protein levels, as well as their roles in lung oncogenesis. Comparative genomic hybridization (CGH) studies revealed chromosome aberration in lung cancer subtypes, including ADC, SCC, LCC, and SCLC. The most common abnormality is 19p loss and 19q gain. Sixty-four aberrant genes identified in previous genomic studies and their encoded protein functions were further validated in the neXtProt database ( http://www.nextprot.org/ ). Among those, the loss of tumor suppressor genes STK11, MUM1, KISS1R (19p13.3), and BRG1 (19p13.13) is associated with lung oncogenesis or remote metastasis. Gene aberrations include translocation t(15, 19) (q13, p13.1) fusion oncogene BRD4-NUT, DNA repair genes (ERCC1, ERCC2, XRCC1), TGFβ1 pathway activation genes (TGFB1, LTBP4), Dyrk1B, and potential oncogenesis protector genes such as NFkB pathway inhibition genes (NFKBIB, PPP1R13L) and EGLN2. In conclusion, neXtProt is an effective resource for the validation of gene aberrations identified in genomic studies. It promises to enhance our understanding of lung cancer oncogenesis.
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Affiliation(s)
- Xiangdong Wang
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University, Shanghai, China,
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10
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Shearer JJ, Wold EA, Umbaugh CS, Lichti CF, Nilsson CL, Figueiredo ML. Inorganic Arsenic-Related Changes in the Stromal Tumor Microenvironment in a Prostate Cancer Cell-Conditioned Media Model. Environ Health Perspect 2016; 124:1009-15. [PMID: 26588813 PMCID: PMC4937864 DOI: 10.1289/ehp.1510090] [Citation(s) in RCA: 14] [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] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 11/12/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND The tumor microenvironment plays an important role in the progression of cancer by mediating stromal-epithelial paracrine signaling, which can aberrantly modulate cellular proliferation and tumorigenesis. Exposure to environmental toxicants, such as inorganic arsenic (iAs), has also been implicated in the progression of prostate cancer. OBJECTIVE The role of iAs exposure in stromal signaling in the tumor microenvironment has been largely unexplored. Our objective was to elucidate molecular mechanisms of iAs-induced changes to stromal signaling by an enriched prostate tumor microenvironment cell population, adipose-derived mesenchymal stem/stromal cells (ASCs). RESULTS ASC-conditioned media (CM) collected after 1 week of iAs exposure increased prostate cancer cell viability, whereas CM from ASCs that received no iAs exposure decreased cell viability. Cytokine array analysis suggested changes to cytokine signaling associated with iAs exposure. Subsequent proteomic analysis suggested a concentration-dependent alteration to the HMOX1/THBS1/TGFβ signaling pathway by iAs. These results were validated by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) and Western blotting, confirming a concentration-dependent increase in HMOX1 and a decrease in THBS1 expression in ASC following iAs exposure. Subsequently, we used a TGFβ pathway reporter construct to confirm a decrease in stromal TGFβ signaling in ASC following iAs exposure. CONCLUSIONS Our results suggest a concentration-dependent alteration of stromal signaling: specifically, attenuation of stromal-mediated TGFβ signaling following exposure to iAs. Our results indicate iAs may enhance prostate cancer cell viability through a previously unreported stromal-based mechanism. These findings indicate that the stroma may mediate the effects of iAs in tumor progression, which may have future therapeutic implications. CITATION Shearer JJ, Wold EA, Umbaugh CS, Lichti CF, Nilsson CL, Figueiredo ML. 2016. Inorganic arsenic-related changes in the stromal tumor microenvironment in a prostate cancer cell-conditioned media model. Environ Health Perspect 124:1009-1015; http://dx.doi.org/10.1289/ehp.1510090.
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Affiliation(s)
- Joseph J. Shearer
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Eric A. Wold
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Charles S. Umbaugh
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Cheryl F. Lichti
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Carol L. Nilsson
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Marxa L. Figueiredo
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
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11
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Hsu WCJ, Scala F, Nenov MN, Wildburger NC, Elferink H, Singh AK, Chesson CB, Buzhdygan T, Sohail M, Shavkunov AS, Panova NI, Nilsson CL, Rudra JS, Lichti CF, Laezza F. CK2 activity is required for the interaction of FGF14 with voltage-gated sodium channels and neuronal excitability. FASEB J 2016; 30:2171-86. [PMID: 26917740 DOI: 10.1096/fj.201500161] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 11/17/2015] [Accepted: 02/09/2016] [Indexed: 01/18/2023]
Abstract
Recent data shows that fibroblast growth factor 14 (FGF14) binds to and controls the function of the voltage-gated sodium (Nav) channel with phenotypic outcomes on neuronal excitability. Mutations in the FGF14 gene in humans have been associated with brain disorders that are partially recapitulated in Fgf14(-/-) mice. Thus, signaling pathways that modulate the FGF14:Nav channel interaction may be important therapeutic targets. Bioluminescence-based screening of small molecule modulators of the FGF14:Nav1.6 complex identified 4,5,6,7 -: tetrabromobenzotriazole (TBB), a potent casein kinase 2 (CK2) inhibitor, as a strong suppressor of FGF14:Nav1.6 interaction. Inhibition of CK2 through TBB reduces the interaction of FGF14 with Nav1.6 and Nav1.2 channels. Mass spectrometry confirmed direct phosphorylation of FGF14 by CK2 at S228 and S230, and mutation to alanine at these sites modified FGF14 modulation of Nav1.6-mediated currents. In 1 d in vitro hippocampal neurons, TBB induced a reduction in FGF14 expression, a decrease in transient Na(+) current amplitude, and a hyperpolarizing shift in the voltage dependence of Nav channel steady-state inactivation. In mature neurons, TBB reduces the axodendritic polarity of FGF14. In cornu ammonis area 1 hippocampal slices from wild-type mice, TBB impairs neuronal excitability by increasing action potential threshold and lowering firing frequency. Importantly, these changes in excitability are recapitulated in Fgf14(-/-) mice, and deletion of Fgf14 occludes TBB-dependent phenotypes observed in wild-type mice. These results suggest that a CK2-FGF14 axis may regulate Nav channels and neuronal excitability.-Hsu, W.-C. J., Scala, F., Nenov, M. N., Wildburger, N. C., Elferink, H., Singh, A. K., Chesson, C. B., Buzhdygan, T., Sohail, M., Shavkunov, A. S., Panova, N. I., Nilsson, C. L., Rudra, J. S., Lichti, C. F., Laezza, F. CK2 activity is required for the interaction of FGF14 with voltage-gated sodium channels and neuronal excitability.
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Affiliation(s)
| | - Federico Scala
- Department of Pharmacology and Toxicology, Institute of Human Physiology, Università Cattolica, Rome, Italy; and
| | | | - Norelle C Wildburger
- Department of Pharmacology and Toxicology, Department of Neurology, Washington, University School of Medicine, St. Louis, Missouri, USA
| | | | | | - Charles B Chesson
- Human Pathophysiology and Translational Medicine, Institute for Translational Sciences
| | | | | | | | | | - Carol L Nilsson
- Department of Pharmacology and Toxicology, Sealy Center for Molecular Medicine
| | | | - Cheryl F Lichti
- Department of Pharmacology and Toxicology, Mitchell Center for Neurodegenerative Diseases
| | - Fernanda Laezza
- Department of Pharmacology and Toxicology, Mitchell Center for Neurodegenerative Diseases, Center for Addiction Research, and Center for Biomedical Engineering, University of Texas Medical Branch, Galveston, Texas, USA;
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12
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Lichti CF, Wildburger NC, Shavkunov AS, Mostovenko E, Liu H, Sulman EP, Nilsson CL. The proteomic landscape of glioma stem-like cells. EuPA Open Proteomics 2015. [DOI: 10.1016/j.euprot.2015.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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13
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Wildburger NC, Lichti CF, LeDuc RD, Schmidt M, Kroes RA, Moskal JR, Nilsson CL. Quantitative proteomics and transcriptomics reveals metabolic differences in attracting and non-attracting human-in-mouse glioma stem cell xenografts and stromal cells. EuPA Open Proteomics 2015. [DOI: 10.1016/j.euprot.2015.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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14
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Wildburger NC, Zhou S, Zacharias LG, Kroes RA, Moskal JR, Schmidt M, Mirzaei P, Gumin J, Lang FF, Mechref Y, Nilsson CL. Integrated Transcriptomic and Glycomic Profiling of Glioma Stem Cell Xenografts. J Proteome Res 2015; 14:3932-9. [PMID: 26185906 DOI: 10.1021/acs.jproteome.5b00549] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 12/28/2022]
Abstract
Bone marrow-derived human mesenchymal stem cells (BM-hMSCs) have the innate ability to migrate or home toward and engraft in tumors such as glioblastoma (GBM). Because of this unique property of BM-hMSCs, we have explored their use for cell-mediated therapeutic delivery for the advancement of GBM treatment. Extravasation, the process by which blood-borne cells—such as BM-hMSCs—enter the tissue, is a highly complex process but is heavily dependent upon glycosylation for glycan-glycan and glycan-protein adhesion between the cell and endothelium. However, in a translationally significant preclinical glioma stem cell xenograft (GSCX) model of GBM, BM-hMSCs demonstrate unequal tropism toward these tumors. We hypothesized that there may be differences in the glycan compositions between the GSCXs that elicit homing ("attractors") and those that do not ("non-attractors") that facilitate or impede the engraftment of BM-hMSCs in the tumor. In this study, glycotranscriptomic analysis revealed significant heterogeneity within the attractor phenotype and the enrichment of high mannose type N-glycan biosynthesis in the non-attractor phenotype. Orthogonal validation with topical PNGase F deglycosylation on the tumor regions of xenograft tissue, followed by nLC-ESI-MS, confirmed the presence of increased high mannose type N-glycans in the non-attractors. Additional evidence provided by our glycomic study revealed the prevalence of terminal sialic acid-containing N-glycans in non-attractors and terminal galactose and N-acetyl-glucosamine N-glycans in attractors. Our results provide the first evidence for differential glycomic profiles in attractor and non-attractor GSCXs and extend the scope of molecular determinates in BM-hMSC homing to glioma.
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Affiliation(s)
| | - Shiyue Zhou
- Department of Chemistry and Biochemistry, Texas Tech University , 2500 Broadway, Lubbock, Texas 79409, United States
| | - Lauren G Zacharias
- Department of Chemistry and Biochemistry, Texas Tech University , 2500 Broadway, Lubbock, Texas 79409, United States
| | - Roger A Kroes
- The Falk Center for Molecular Therapeutics, McCormick School of Engineering and Applied Sciences, Northwestern University , 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Joseph R Moskal
- The Falk Center for Molecular Therapeutics, McCormick School of Engineering and Applied Sciences, Northwestern University , 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Mary Schmidt
- The Falk Center for Molecular Therapeutics, McCormick School of Engineering and Applied Sciences, Northwestern University , 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Parvin Mirzaei
- Department of Chemistry and Biochemistry, Texas Tech University , 2500 Broadway, Lubbock, Texas 79409, United States
| | - Joy Gumin
- Department of Neurosurgery and The Brain Tumor Center, The University of Texas M.D. Anderson Cancer Center , 1515 Holcombe Boulevard, Houston, Texas 77030, United States
| | - Frederick F Lang
- Department of Neurosurgery and The Brain Tumor Center, The University of Texas M.D. Anderson Cancer Center , 1515 Holcombe Boulevard, Houston, Texas 77030, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University , 2500 Broadway, Lubbock, Texas 79409, United States
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15
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Horvatovich P, Végvári Á, Saul J, Park JG, Qiu J, Syring M, Pirrotte P, Petritis K, Tegeler TJ, Aziz M, Fuentes M, Diez P, Gonzalez-Gonzalez M, Ibarrola N, Droste C, De Las Rivas J, Gil C, Clemente F, Hernaez ML, Corrales FJ, Nilsson CL, Berven FS, Bischoff R, Fehniger TE, LaBaer J, Marko-Varga G. In Vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins. J Proteome Res 2015; 14:3441-51. [PMID: 26155874 DOI: 10.1021/acs.jproteome.5b00486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Approximately 18% of all human genes purported to encode proteins have not been directly evidenced at the protein level, according to the validation criteria established by neXtProt, and are considered to be "missing" proteins. One of the goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to identify as many of these missing proteins as possible in human samples using mass spectrometry-based methods. To further this goal, a consortium of C-HPP teams (chromosomes 5, 10, 16, and 19) has joined forces to devise new strategies to identify missing proteins by use of a cell-free in vitro transcription/translation system (IVTT). The proposed strategy employs LC-MS/MS data-dependent acquisition (DDA) and targeted selective reaction monitoring (SRM) methods to scrutinize low-complexity samples derived from IVTT. The optimized assays are then applied to identify missing proteins in human cells and tissues. We describe the approach and show proof-of-concept results for development of LC-SRM assays for identification of 18 missing proteins. We believe that the IVTT system, when coupled with downstream mass spectrometric identification, can be applied to identify proteins that have eluded more traditional methods of detection.
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Affiliation(s)
- Péter Horvatovich
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ákos Végvári
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | - Justin Saul
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Jin G Park
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Ji Qiu
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Michael Syring
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Patrick Pirrotte
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Konstantinos Petritis
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States.,Pathology Research, Phoenix Children's Hospital , 1919 East Thomas Road, Phoenix, Arizona 85016, United States
| | - Tony J Tegeler
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Meraj Aziz
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | | | | | | | | | | | | | - Concha Gil
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Felipe Clemente
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Maria Luisa Hernaez
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Fernando J Corrales
- Center for Applied Medical Research (CIMA), University of Navarra, PRB2-ProteoRed-ISCIII, IDISNA, Ciberhed , 31008 Pamplona, Spain
| | - Carol L Nilsson
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen , Postbox 7804, N-5009 Bergen, Norway.,The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Postbox 1400, 5021 Bergen, Norway
| | - Rainer Bischoff
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | - Joshua LaBaer
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - György Marko-Varga
- First Department of Surgery, Tokyo Medical University , 6-7-1 Nishishinjuku Shinjuku-ku, 160-0023 Tokyo, Japan
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16
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Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, He QY, Menon R, Guan Y, Corrales FJ, Segura V, Casal JI, Pascual-Montano A, Albar JP, Fuentes M, Gonzalez-Gonzalez M, Diez P, Ibarrola N, Degano RM, Mohammed Y, Borchers CH, Urbani A, Soggiu A, Yamamoto T, Salekdeh GH, Archakov A, Ponomarenko E, Lisitsa A, Lichti CF, Mostovenko E, Kroes RA, Rezeli M, Végvári Á, Fehniger TE, Bischoff R, Vizcaíno JA, Deutsch EW, Lane L, Nilsson CL, Marko-Varga G, Omenn GS, Jeong SK, Lim JS, Paik YK, Hancock WS. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project. J Proteome Res 2015; 14:3415-31. [DOI: 10.1021/pr5013009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Péter Horvatovich
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9713 AV Groningen, The Netherlands
| | - Emma K. Lundberg
- Science
for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Taipei 115, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, 128 Academia Road Sec. 2, Taipei 115, Taiwan
| | - Fuchu He
- The State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Edouard C. Nice
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Robert J. Goode
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Simon Yu
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Shoba Ranganathan
- Department
of Chemistry and Biomolecular Sciences and ARC Centre of Excellence
in Bioinformatics, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Mark S. Baker
- Australian
School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Gilberto B. Domont
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Av Athos da Silveira Ramos 149, CT-A542, 21941-909 Rio de Janeriro, Rj, Brazil
| | - Erika Velasquez
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Av Athos da Silveira Ramos 149, CT-A542, 21941-909 Rio de Janeriro, Rj, Brazil
| | - Dong Li
- The State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Siqi Liu
- Beijing Institute of Genomics and BGI Shenzhen, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- BGI Shenzhen, Beishan Road, Yantian District, Shenzhen, 518083, China
| | - Quanhui Wang
- Beijing Institute of Genomics and BGI Shenzhen, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein
Research of Guangdong
Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Rajasree Menon
- Department of Computational Medicine & Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Yuanfang Guan
- Departments of Computational Medicine & Bioinformatics and Computer Sciences, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Fernando J. Corrales
- ProteoRed-ISCIII,
Biomolecular and Bioinformatics Resources Platform (PRB2), Spanish
Consortium of C-HPP (Chr-16), CIMA, University of Navarra, 31008 Pamplona, Spain
- Chr16 SpHPP Consortium, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Victor Segura
- ProteoRed-ISCIII,
Biomolecular and Bioinformatics Resources Platform (PRB2), Spanish
Consortium of C-HPP (Chr-16), CIMA, University of Navarra, 31008 Pamplona, Spain
- Chr16 SpHPP Consortium, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - J. Ignacio Casal
- Department
of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), 28040 Madrid, Spain
| | | | - Juan P. Albar
- Centro Nacional de Biotecnologia (CNB-CSIC), Cantoblanco, 28049 Madrid, Spain
| | - Manuel Fuentes
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Maria Gonzalez-Gonzalez
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Paula Diez
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Nieves Ibarrola
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Rosa M. Degano
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics
Centre, Vancouver Island
Technology Park, #3101−4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christoph H. Borchers
- University of Victoria-Genome British Columbia Proteomics
Centre, Vancouver Island
Technology Park, #3101−4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
| | - Andrea Urbani
- Proteomics
and Metabonomic, Laboratory, Fondazione Santa Lucia, Rome, Italy
- Department
of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | - Alessio Soggiu
- Department
of Veterinary Science and Public Health (DIVET), University of Milano, via Celoria 10, 20133 Milano, Italy
| | - Tadashi Yamamoto
- Institute
of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | | | | | - Andrey Lisitsa
- Orechovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Cheryl F. Lichti
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - Ekaterina Mostovenko
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - Roger A. Kroes
- Falk Center for Molecular Therapeutics, Department of Biomedical Engineering, Northwestern University, 1801 Maple Ave., Suite 4300, Evanston, Illinois 60201, United States
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Ákos Végvári
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Thomas E. Fehniger
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9713 AV Groningen, The Netherlands
| | - Juan Antonio Vizcaíno
- European Molecular
Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, United Kingdom
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Department
of Human Protein Science, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Carol L. Nilsson
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Gilbert S. Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics and School of Public Health, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Seul-Ki Jeong
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - Jong-Sun Lim
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - Young-Ki Paik
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - William S. Hancock
- The
Barnett Institute of Chemical and Biological Analysis, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
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17
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Wang X, Zhang Y, Nilsson CL, Berven FS, Andrén PE, Carlsohn E, Horvatovich P, Malm J, Fuentes M, Végvári Á, Welinder C, Fehniger TE, Rezeli M, Edula G, Hober S, Nishimura T, Marko-Varga G. Erratum to: Association of chromosome 19 to lung cancer genotypes and phenotypes. Cancer Metastasis Rev 2015; 34:227. [PMID: 26143031 DOI: 10.1007/s10555-015-9571-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Erratum to: Cancer and Metastasis Review, DOI 10.1007/s10555-015-9556-2. There are changes in authors' affiliations and a new affiliations for Carol L. Nilsson and Thomas E. Fehniger has been added. The corresponding author also missed out to include Peter Horvatovich as a co-author of this work. The complete list of authors is now listed above.
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Affiliation(s)
- Xiangdong Wang
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University, Shanghai, China,
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18
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Wildburger NC, Wood PL, Gumin J, Lichti CF, Emmett MR, Lang FF, Nilsson CL. ESI-MS/MS and MALDI-IMS Localization Reveal Alterations in Phosphatidic Acid, Diacylglycerol, and DHA in Glioma Stem Cell Xenografts. J Proteome Res 2015; 14:2511-9. [PMID: 25880480 DOI: 10.1021/acs.jproteome.5b00076] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Glioblastoma (GBM) is the most common adult primary brain tumor. Despite aggressive multimodal therapy, the survival of patients with GBM remains dismal. However, recent evidence has demonstrated the promise of bone marrow-derived mesenchymal stem cells (BM-hMSCs) as a therapeutic delivery vehicle for anti-glioma agents due to their ability to migrate or home to human gliomas. While several studies have demonstrated the feasibility of harnessing the homing capacity of BM-hMSCs for targeted delivery of cancer therapeutics, it is now also evident, based on clinically relevant glioma stem cell (GSC) models of GBMs, that BM-hMSCs demonstrate variable tropism toward these tumors. In this study, we compared the lipid environment of GSC xenografts that attract BM-hMSCs (N = 9) with those that do not attract (N = 9) to identify lipid modalities that are conducive to homing of BM-hMSC to GBMs. We identified lipids directly from tissue by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) and electrospray ionization-tandem mass spectrometry (ESI-MS/MS) of lipid extracts. Several species of signaling lipids, including phosphatidic acid (PA 36:2, PA 40:5, PA 42:5, and PA 42:7) and diacylglycerol (DAG 34:0, DAG 34:1, DAG 36:1, DAG 38:4, DAG 38:6, and DAG 40:6), were lower in attracting xenografts. Molecular lipid images showed that PA (36:2), DAG (40:6), and docosahexaenoic acid (DHA) were decreased within tumor regions of attracting xenografts. Our results provide the first evidence for lipid signaling pathways and lipid-mediated tumor inflammatory responses in the homing of BM-hMSCs to GSC xenografts. Our studies provide new fundamental knowledge on the molecular correlates of the differential homing capacity of BM-hMSCs toward GSC xenografts.
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Affiliation(s)
| | - Paul L Wood
- ∥Department of Physiology and Pharmacology, Lincoln Memorial University, 6965 Cumberland Gap Parkway, Harrogate, Tennessee 37752, United States
| | | | - Cheryl F Lichti
- §UTMB Cancer Center, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | - Mark R Emmett
- §UTMB Cancer Center, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | | | - Carol L Nilsson
- §UTMB Cancer Center, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1074, United States
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19
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Wildburger NC, Ali SR, Hsu WCJ, Shavkunov AS, Nenov MN, Lichti CF, LeDuc RD, Mostovenko E, Panova-Elektronova NI, Emmett MR, Nilsson CL, Laezza F. Quantitative proteomics reveals protein-protein interactions with fibroblast growth factor 12 as a component of the voltage-gated sodium channel 1.2 (nav1.2) macromolecular complex in Mammalian brain. Mol Cell Proteomics 2015; 14:1288-300. [PMID: 25724910 PMCID: PMC4424400 DOI: 10.1074/mcp.m114.040055] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [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: 04/02/2014] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated sodium channels (Nav1.1–Nav1.9) are responsible for the initiation and propagation of action potentials in neurons, controlling firing patterns, synaptic transmission and plasticity of the brain circuit. Yet, it is the protein–protein interactions of the macromolecular complex that exert diverse modulatory actions on the channel, dictating its ultimate functional outcome. Despite the fundamental role of Nav channels in the brain, information on its proteome is still lacking. Here we used affinity purification from crude membrane extracts of whole brain followed by quantitative high-resolution mass spectrometry to resolve the identity of Nav1.2 protein interactors. Of the identified putative protein interactors, fibroblast growth factor 12 (FGF12), a member of the nonsecreted intracellular FGF family, exhibited 30-fold enrichment in Nav1.2 purifications compared with other identified proteins. Using confocal microscopy, we visualized native FGF12 in the brain tissue and confirmed that FGF12 forms a complex with Nav1.2 channels at the axonal initial segment, the subcellular specialized domain of neurons required for action potential initiation. Co-immunoprecipitation studies in a heterologous expression system validate Nav1.2 and FGF12 as interactors, whereas patch-clamp electrophysiology reveals that FGF12 acts synergistically with CaMKII, a known kinase regulator of Nav channels, to modulate Nav1.2-encoded currents. In the presence of CaMKII inhibitors we found that FGF12 produces a bidirectional shift in the voltage-dependence of activation (more depolarized) and the steady-state inactivation (more hyperpolarized) of Nav1.2, increasing the channel availability. Although providing the first characterization of the Nav1.2 CNS proteome, we identify FGF12 as a new functionally relevant interactor. Our studies will provide invaluable information to parse out the molecular determinant underlying neuronal excitability and plasticity, and extending the relevance of iFGFs signaling in the normal and diseased brain.
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Affiliation(s)
- Norelle C Wildburger
- From the ‡Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555-0617; §Neuroscience Graduate Program, Graduate School of Biomedical Sciences, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas, 77555-0617; ¶UTMB Cancer Center, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas, 77555-1074;
| | - Syed R Ali
- From the ‡Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555-0617
| | - Wei-Chun J Hsu
- ‖Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas, 77555-0617
| | - Alexander S Shavkunov
- From the ‡Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555-0617; ¶UTMB Cancer Center, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas, 77555-1074
| | - Miroslav N Nenov
- From the ‡Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555-0617
| | - Cheryl F Lichti
- From the ‡Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555-0617; ¶UTMB Cancer Center, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas, 77555-1074
| | - Richard D LeDuc
- **National Center for Genome Analysis Support, Indiana University, 107 S Indiana Ave., Bloomington, Indiana, 47408
| | - Ekaterina Mostovenko
- From the ‡Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555-0617; ¶UTMB Cancer Center, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas, 77555-1074
| | - Neli I Panova-Elektronova
- From the ‡Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555-0617
| | - Mark R Emmett
- ¶UTMB Cancer Center, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas, 77555-1074; ‖Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas, 77555-0617
| | - Carol L Nilsson
- From the ‡Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555-0617; ¶UTMB Cancer Center, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas, 77555-1074
| | - Fernanda Laezza
- From the ‡Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555-0617;
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20
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James TF, Nenov MN, Wildburger NC, Lichti CF, Luisi J, Vergara F, Panova-Electronova NI, Nilsson CL, Rudra JS, Green TA, Labate D, Laezza F. The Nav1.2 channel is regulated by GSK3. Biochim Biophys Acta Gen Subj 2015; 1850:832-44. [PMID: 25615535 DOI: 10.1016/j.bbagen.2015.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/17/2014] [Accepted: 01/14/2015] [Indexed: 12/19/2022]
Abstract
BACKGROUND Phosphorylation plays an essential role in regulating voltage-gated sodium (Na(v)) channels and excitability. Yet, a surprisingly limited number of kinases have been identified as regulators of Na(v) channels. We posited that glycogen synthase kinase 3 (GSK3), a critical kinase found associated with numerous brain disorders, might directly regulate neuronal Na(v) channels. METHODS We used patch-clamp electrophysiology to record sodium currents from Na(v)1.2 channels stably expressed in HEK-293 cells. mRNA and protein levels were quantified with RT-PCR, Western blot, or confocal microscopy, and in vitro phosphorylation and mass spectrometry to identify phosphorylated residues. RESULTS We found that exposure of cells to GSK3 inhibitor XIII significantly potentiates the peak current density of Na(v)1.2, a phenotype reproduced by silencing GSK3 with siRNA. Contrarily, overexpression of GSK3β suppressed Na(v)1.2-encoded currents. Neither mRNA nor total protein expression was changed upon GSK3 inhibition. Cell surface labeling of CD4-chimeric constructs expressing intracellular domains of the Na(v)1.2 channel indicates that cell surface expression of CD4-Na(v)1.2 C-tail was up-regulated upon pharmacological inhibition of GSK3, resulting in an increase of surface puncta at the plasma membrane. Finally, using in vitro phosphorylation in combination with high resolution mass spectrometry, we further demonstrate that GSK3β phosphorylates T(1966) at the C-terminal tail of Na(v)1.2. CONCLUSION These findings provide evidence for a new mechanism by which GSK3 modulates Na(v) channel function via its C-terminal tail. GENERAL SIGNIFICANCE These findings provide fundamental knowledge in understanding signaling dysfunction common in several neuropsychiatric disorders.
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Affiliation(s)
- Thomas F James
- Department of Pharmacology & Toxicology, USA; Neuroscience Graduate Program, USA
| | | | - Norelle C Wildburger
- Department of Pharmacology & Toxicology, USA; Neuroscience Graduate Program, USA
| | | | | | | | | | | | - Jai S Rudra
- Department of Pharmacology & Toxicology, USA
| | - Thomas A Green
- Department of Pharmacology & Toxicology, USA; Center for Addiction Research, USA
| | | | - Fernanda Laezza
- Department of Pharmacology & Toxicology, USA; Center for Addiction Research, USA; Center for Biomedical Engineering, USA; Mitchell Center for Neurodegenerative Diseases, USA.
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21
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Nilsson CL, Mostovenko E, Lichti CF, Ruggles K, Fenyö D, Rosenbloom KR, Hancock WS, Paik YK, Omenn GS, LaBaer J, Kroes RA, Uhlén M, Hober S, Végvári Á, Andrén PE, Sulman EP, Lang FF, Fuentes M, Carlsohn E, Emmett MR, Moskal JR, Berven FS, Fehniger TE, Marko-Varga G. Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome. J Proteome Res 2014; 14:603-8. [DOI: 10.1021/pr500564q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | | | - Kelly Ruggles
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, New York, Santa Cruz California 95064, United States
| | - David Fenyö
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, New York, Santa Cruz California 95064, United States
| | - Kate R. Rosenbloom
- Center
for Biomolecular Science and Engineering, University of California, 1156 High St, Mail Stop CBSE, Santa Cruz, California 95064, United States
| | - William S. Hancock
- College
of Science, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Young-Ki Paik
- Department
of Biochemistry, Yonsei Proteome Research Center, 50 Yonsei-Ro,
Seodaemun-gu, Seoul 120-749, South Korea
| | - Gilbert S. Omenn
- Center for
Computational Medicine and Bioinformatics, University of Michican Medical School, 100 Washtenaw Avenue, Ann
Arbor, Michigan 48109, United States
| | - Joshua LaBaer
- Biodesign
Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287, United States
| | - Roger A. Kroes
- The
Falk Center for Molecular Therapeutics, McCormick School of Engineering
and Applied Sciences, Northwestern University, 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Matthias Uhlén
- Biotechnology,
AlbaNova University Center, Royal Institute of Technology, Roslagstullsbacken
21, 106 91 Stockholm, Sweden
| | - Sophia Hober
- School
of Biotechnology, Department of Proteomics, Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Ákos Végvári
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, 221 84 Lund, Sweden
| | - Per E. Andrén
- Department
of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Erik P. Sulman
- Department
of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, United States
| | - Frederick F. Lang
- Department
of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, United States
| | - Manuel Fuentes
- Centro
de Investigacion del Cancer, Medicine-Immunology, CSIC-University of Salamanca, Salamanca 37007, Spain
| | - Elisabet Carlsohn
- Proteomics
Core Facility, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan
7A, Gothenburg 413 90, Sweden
| | | | - Joseph R. Moskal
- The
Falk Center for Molecular Therapeutics, McCormick School of Engineering
and Applied Sciences, Northwestern University, 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Frode S. Berven
- Department
of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Thomas E. Fehniger
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, 221 84 Lund, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, 221 84 Lund, Sweden
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22
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Meyer-Baese A, Wildberger J, Meyer-Baese U, Nilsson CL. Data analysis techniques in phosphoproteomics. Electrophoresis 2014; 35:3452-62. [DOI: 10.1002/elps.201400219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Anke Meyer-Baese
- Department of Scientific Computing; Florida State University; FL USA
| | - Joachim Wildberger
- Department of Radiology; Maastricht University Medical Center; Maastricht The Netherlands
| | - Uwe Meyer-Baese
- Department of Electrical and Computer Engineering; Florida State University; FL USA
| | - Carol L. Nilsson
- Departments of Pharmacology and Toxicology and Biochemistry and Molecular Biology; UTMB; and UTMB Cancer Center; University of Texas; Medical Branch at Galveston; TX USA
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23
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Lichti CF, Mostovenko E, Wadsworth PA, Lynch GC, Pettitt BM, Sulman EP, Wang Q, Lang FF, Rezeli M, Marko-Varga G, Végvári Á, Nilsson CL. Systematic identification of single amino acid variants in glioma stem-cell-derived chromosome 19 proteins. J Proteome Res 2014; 14:778-86. [PMID: 25399873 PMCID: PMC4324435 DOI: 10.1021/pr500810g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 12/15/2022]
Abstract
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Novel
proteoforms with single amino acid variations represent proteins
that often have altered biological functions but are less explored
in the human proteome. We have developed an approach, searching high
quality shotgun proteomic data against an extended protein database,
to identify expressed mutant proteoforms in glioma stem cell (GSC)
lines. The systematic search of MS/MS spectra using PEAKS 7.0 as the
search engine has recognized 17 chromosome 19 proteins in GSCs with
altered amino acid sequences. The results were further verified by
manual spectral examination, validating 19 proteoforms. One of the
novel findings, a mutant form of branched-chain aminotransferase 2
(p.Thr186Arg), was verified at the transcript level
and by targeted proteomics in several glioma stem cell lines. The
structure of this proteoform was examined by molecular modeling in
order to estimate conformational changes due to mutation that might
lead to functional modifications potentially linked to glioma. Based
on our initial findings, we believe that our approach presented could
contribute to construct a more complete map of the human functional
proteome.
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Affiliation(s)
- Cheryl F Lichti
- Department of Pharmacology and Toxicology and ‡Biochemistry and Molecular Biology, UTMB Cancer Center, University of Texas Medical Branch , Galveston, Texas 77555, United States
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24
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Lichti CF, Wildburger NC, Emmett MR, Mostovenko E, Shavkunov AS, Strain SK, Nilsson CL. Post-translational Modifications in the Human Proteome. Translational Bioinformatics 2014. [DOI: 10.1007/978-94-017-9202-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Lichti CF, Liu H, Shavkunov AS, Mostovenko E, Sulman EP, Ezhilarasan R, Wang Q, Kroes RA, Moskal JC, Fenyö D, Oksuz BA, Conrad CA, Lang FF, Berven FS, Végvári A, Rezeli M, Marko-Varga G, Hober S, Nilsson CL. Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines. J Proteome Res 2013; 13:191-9. [PMID: 24266786 DOI: 10.1021/pr400786s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One subproject within the global Chromosome 19 Consortium is to define chromosome 19 gene and protein expression in glioma-derived cancer stem cells (GSCs). Chromosome 19 is notoriously linked to glioma by 1p/19q codeletions, and clinical tests are established to detect that specific aberration. GSCs are tumor-initiating cells and are hypothesized to provide a repository of cells in tumors that can self-replicate and be refractory to radiation and chemotherapeutic agents developed for the treatment of tumors. In this pilot study, we performed RNA-Seq, label-free quantitative protein measurements in six GSC lines, and targeted transcriptomic analysis using a chromosome 19-specific microarray in an additional six GSC lines. The data have been deposited to the ProteomeXchange with identifier PXD000563. Here we present insights into differences in GSC gene and protein expression, including the identification of proteins listed as having no or low evidence at the protein level in the Human Protein Atlas, as correlated to chromosome 19 and GSC subtype. Furthermore, the upregulation of proteins downstream of adenovirus-associated viral integration site 1 (AAVS1) in GSC11 in response to oncolytic adenovirus treatment was demonstrated. Taken together, our results may indicate new roles for chromosome 19, beyond the 1p/19q codeletion, in the future of personalized medicine for glioma patients.
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Affiliation(s)
- Cheryl F Lichti
- Department of Pharmacology and Toxicology, UTMB Cancer Center, University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555, United States
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26
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Liu H, Lichti CF, Mirfattah B, Frahm J, Nilsson CL. A modified database search strategy leads to improved identification of in vitro brominated peptides spiked into a complex proteomic sample. J Proteome Res 2013; 12:4248-54. [PMID: 23898862 DOI: 10.1021/pr400472c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Inflammation leads to activation of immune cells, resulting in production of hypobromous acid. Few investigations have been performed on protein bromination on a proteomic scale, even though bromination is a relatively abundant protein modification in endogenously brominated proteomes. Such studies have been hampered by the lack of an optimized database search strategy. In order to address this issue, we performed nano-LC-MS/MS analysis of an in vitro generated, trypsin-digested brominated human serum albumin standard, spiked into a complex trypsin-digested proteomic background, in an LTQ-Orbitrap instrument. We found that brominated peptides spiked in at a 1-10% ratio (mass:mass) were easily identified by manual inspection when higher-energy collisional dissociation (HCD) and collision induced dissociation (CID) were employed as the dissociation mode; however, confident assignment of brominated peptides from protein database searches required a novel approach. By addition of a custom modification, corresponding to the substitution of a single bromine with 81Br rather than 79Br for dibromotyrosine (79Br81BrY), the number of validated assignments for peptides containing dibromotyrosine increased significantly when analyzing both high resolution and low resolution MS/MS data. This new approach will facilitate the identification of proteins derived from endogenously brominated proteomes, providing further knowledge about the role of protein bromination in various pathological states.
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Affiliation(s)
- Huiling Liu
- University of Texas Medical Branch, Department of Pharmacology and Toxicology, 301 University Boulevard, Galveston, Texas 77555-0617, United States
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27
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Nilsson CL, Berven F, Selheim F, Liu H, Moskal JR, Kroes RA, Sulman EP, Conrad CA, Lang FF, Andrén PE, Nilsson A, Carlsohn E, Lilja H, Malm J, Fenyö D, Subramaniyam D, Wang X, Gonzales-Gonzales M, Dasilva N, Diez P, Fuentes M, Végvári Á, Sjödin K, Welinder C, Laurell T, Fehniger TE, Lindberg H, Rezeli M, Edula G, Hober S, Marko-Varga G. Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium. J Proteome Res 2012; 12:135-50. [PMID: 23249167 DOI: 10.1021/pr3008607] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A first research development progress report of the Chromosome 19 Consortium with members from Sweden, Norway, Spain, United States, China and India, a part of the Chromosome-centric Human Proteome Project (C-HPP) global initiative, is presented ( http://www.c-hpp.org ). From the chromosome 19 peptide-targeted library constituting 6159 peptides, a pilot study was conducted using a subset with 125 isotope-labeled peptides. We applied an annotation strategy with triple quadrupole, ESI-Qtrap, and MALDI mass spectrometry platforms, comparing the quality of data within and in between these instrumental set-ups. LC-MS conditions were outlined by multiplex assay developments, followed by MRM assay developments. SRM was applied to biobank samples, quantifying kallikrein 3 (prostate specific antigen) in plasma from prostate cancer patients. The antibody production has been initiated for more than 1200 genes from the entire chromosome 19, and the progress developments are presented. We developed a dedicated transcript microarray to serve as the mRNA identifier by screening cancer cell lines. NAPPA protein arrays were built to align with the transcript data with the Chromosome 19 NAPPA chip, dedicated to 90 proteins, as the first development delivery. We have introduced an IT-infrastructure utilizing a LIMS system that serves as the key interface for the research teams to share and explore data generated within the project. The cross-site data repository will form the basis for sample processing, including biological samples as well as patient samples from national Biobanks.
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Affiliation(s)
- Carol L Nilsson
- Department of Pharmacology and Toxicology, UTMB Cancer Center, University of Texas Medical Branch, Galveston, Texas 77555, United States
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28
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Cardoso R, Love R, Nilsson CL, Bergqvist S, Nowlin D, Yan J, Liu KKC, Zhu J, Chen P, Deng YL, Dyson HJ, Greig MJ, Brooun A. Identification of Cys255 in HIF-1α as a novel site for development of covalent inhibitors of HIF-1α/ARNT PasB domain protein-protein interaction. Protein Sci 2012; 21:1885-96. [PMID: 23033253 DOI: 10.1002/pro.2172] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 12/11/2022]
Abstract
The heterodimer HIF-1α (hypoxia inducible factor)/HIF-β (also known as ARNT-aryl hydrocarbon nuclear translocator) is a key mediator of cellular response to hypoxia. The interaction between these monomer units can be modified by the action of small molecules in the binding interface between their C-terminal heterodimerization (PasB) domains. Taking advantage of the presence of several cysteine residues located in the allosteric cavity of HIF-1α PasB domain, we applied a cysteine-based reactomics "hotspot identification" strategy to locate regions of HIF-1α PasB domain critical for its interaction with ARNT. COMPOUND 5 was identified using a mass spectrometry-based primary screening strategy and was shown to react specifically with Cys255 of the HIF-1α PasB domain. Biophysical characterization of the interaction between PasB domains of HIF-1α and ARNT revealed that covalent binding of COMPOUND 5 to Cys255 reduced binding affinity between HIF-1α and ARNT PasB domains approximately 10-fold. Detailed NMR structural analysis of HIF-1α-PasB-COMPOUND 5 conjugate showed significant local conformation changes in the HIF-1α associated with key residues involved in the HIF-1α/ARNT PasB domain interaction as revealed by the crystal structure of the HIF-1α/ARNT PasB heterodimer. Our screening strategy could be applied to other targets to identify pockets surrounding reactive cysteines suitable for development of small molecule modulators of protein function.
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Affiliation(s)
- Rosa Cardoso
- Oncology Chemistry, Worldwide Research and Development, Pfizer Inc., San Diego, California 92121, USA
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29
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30
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Affiliation(s)
- Carol L Nilsson
- Department of Pharmacology & Toxicology, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas 77555-0617, United States.
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31
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Dillon R, Nilsson CL, Shi SDH, Lee NV, Krastins B, Greig MJ. Discovery of a Novel B-Raf Fusion Protein Related to c-Met Drug Resistance. J Proteome Res 2011; 10:5084-94. [DOI: 10.1021/pr200498v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Carol L. Nilsson
- University of Texas Medical Branch, Galveston, TX 77555, United States
| | | | - Nathan V. Lee
- Pfizer Global Research and Development, La Jolla, California 92121, United States
| | - Bryan Krastins
- Biomarker Research Initiatives in Mass Spectrometry (BRIMS), Thermo Fisher Scientific, Cambridge, Massachusetts 02139, United States
| | - Michael J. Greig
- Pfizer Global Research and Development, La Jolla, California 92121, United States
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32
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He H, Nilsson CL, Emmett MR, Marshall AG, Kroes RA, Moskal JR, Ji Y, Colman H, Priebe W, Lang FF, Conrad CA. Glycomic and transcriptomic response of GSC11 glioblastoma stem cells to STAT3 phosphorylation inhibition and serum-induced differentiation. J Proteome Res 2010; 9:2098-108. [PMID: 20199106 DOI: 10.1021/pr900793a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [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
A glioblastoma stem cell (GSC) line, GSC11, grows as neurospheres in serum-free media supplemented with EGF (epidermal growth factor) and bFGF (basic fibroblast growth factor), and, if implanted in nude mice brains, will recapitulate high-grade glial tumors. Treatment with a STAT3 (signal transducer and activator of transcription 3) phosphorylation inhibitor (WP1193) or 10% FBS (fetal bovine serum) both led to a decrease in expression of the stem cell marker CD133 in GSC11 cells, but differed in phenotype changes. Altered glycolipid profiles were associated with some differentially expressed glycogenes. In serum treated cells, an overall increase in glycosphingolipids may be due to increased expression of ST6GALNAC2, a sialyltransferase. Serum treated cells express more phosphatidylcholine (PC), short chain sphingomyelin (SM) and unsaturated long chain phosphatidylinositol (PI). Decrease of a few glycosphingolipids in the STAT3 phosphorylation inhibited cells may be linked to decreased transcripts of ST6GALNAC2 and UGCGL2, a glucosylceramide synthase. A rare 3-sulfoglucuronylparagloboside carrying HNK1 (human natural killer-1) epitope was found expressed in the GSC11 and the phenotypically differentiated cells. Its up-regulation correlates with increased transcripts of a HNK1 biosynthesis gene, B3GAT2 after serum treatment. Taken together with a quantitative phosphoproteomic study of the same GSC line (C. L. Nilsson, et al. J. Proteome Res. 2010, 9, 430-443), this report represents the most complete systems biology study of cancer stem cell (CSC) differentiation to date. The synergies derived by the combination of glycomic, transcriptomic and phosphoproteomic data may aid our understanding of intracellular and cell-surface events associated with CSC differentiation.
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Affiliation(s)
- Huan He
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, USA
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33
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Nilsson CL, Dillon R, Devakumar A, Shi SDH, Greig M, Rogers JC, Krastins B, Rosenblatt M, Kilmer G, Major M, Kaboord BJ, Sarracino D, Rezai T, Prakash A, Lopez M, Ji Y, Priebe W, Lang FF, Colman H, Conrad CA. Quantitative phosphoproteomic analysis of the STAT3/IL-6/HIF1alpha signaling network: an initial study in GSC11 glioblastoma stem cells. J Proteome Res 2010; 9:430-43. [PMID: 19899826 DOI: 10.1021/pr9007927] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Initiation and maintenance of several cancers including glioblastoma (GBM) may be driven by a small subset of cells called cancer stem cells (CSCs). CSCs may provide a repository of cells in tumor cell populations that are refractory to chemotherapeutic agents developed for the treatment of tumors. STAT3 is a key transcription factor associated with regulation of multiple stem cell types. Recently, a novel autocrine loop (IL-6/STAT3/HIF1alpha) has been observed in multiple tumor types (pancreatic, prostate, lung, and colon). The objective of this study was to probe perturbations of this loop in a glioblastoma cancer stem cell line (GSC11) derived from a human tumor by use of a JAK2/STAT3 phosphorylation inhibitor (WP1193), IL-6 stimulation, and hypoxia. A quantitative phosphoproteomic approach that employed phosphoprotein enrichment, chemical tagging with isobaric tags, phosphopeptide enrichment, and tandem mass spectrometry in a high-resolution instrument was applied. A total of 3414 proteins were identified in this study. A rapid Western blotting technique (<1 h) was used to confirm alterations in key protein expression and phosphorylation levels observed in the mass spectrometric experiments. About 10% of the phosphoproteins were linked to the IL-6 pathway, and the majority of remaining proteins could be assigned to other interlinked networks. By multiple comparisons between the sample conditions, we observed expected changes and gained novel insights into the contribution of each factor to the IL6/STAT3/HIF1alpha autocrine loop and the CSC response to perturbations by hypoxia, inhibition of STAT3 phosphorylation, and IL-6 stimulation.
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Affiliation(s)
- Carol L Nilsson
- Pfizer Global Research and Development, 10770 Science Center Drive, San Diego, California 92121, USA.
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34
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Sihlbom C, Davidsson P, Sjögren M, Wahlund LO, Nilsson CL. Structural and quantitative comparison of cerebrospinal fluid glycoproteins in Alzheimer's disease patients and healthy individuals. Neurochem Res 2008; 33:1332-40. [PMID: 18288611 DOI: 10.1007/s11064-008-9588-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Accepted: 01/02/2008] [Indexed: 10/22/2022]
Abstract
Glycoproteins in cerebrospinal fluid (CSF) are altered in Alzheimer's Disease (AD) patients compared to control individuals. We have utilized albumin depletion prior to 2D gel electrophoresis to enhance glycoprotein concentration for image analysis as well as structural glycoprotein determination without glycan release using mass spectrometry (MS). The benefits of a direct glycoprotein analysis approach include minimal sample manipulation and retention of structural details. A quantitative comparison of gel-separated glycoprotein isoforms from twelve AD patients and twelve control subjects was performed with glycoprotein-specific and total protein stains. We have also compared glycoforms in pooled CSF obtained from AD patients and control subjects with mass spectrometry. One isoform of alpha1-antitrypsin showed decreased glycosylation in AD patients while another glycosylated isoform of an unassigned protein was up-regulated. Protein expression levels of alpha1-antitrypsin were decreased, while the protein levels of apolipoprotein E and clusterin were increased in AD. No specific glycoform could be specifically assigned to AD.
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Affiliation(s)
- Carina Sihlbom
- Department of Medical Chemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at Goteborg University, 440, SE-405 30 Goteborg, Sweden.
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35
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Woodling KA, Eyler JR, Tsybin YO, Nilsson CL, Marshall AG, Edison AS, Al-Naggar IM, Bubb MR. Identification of single and double sites of phosphorylation by ECD FT-ICR/MS in peptides related to the phosphorylation site domain of the myristoylated alanine-rich C kinase protein. J Am Soc Mass Spectrom 2007; 18:2137-2145. [PMID: 17962038 DOI: 10.1016/j.jasms.2007.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Revised: 09/16/2007] [Accepted: 09/17/2007] [Indexed: 05/25/2023]
Abstract
A series of phosphorylated test peptides was studied by electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry (ECD FT-ICR MS). The extensive ECD-induced fragmentation made identification of phosphorylation sites for these peptides straightforward. The site(s) of initial phosphorylation of a synthetic peptide with a sequence identical to that of the phosphorylation site domain (PSD) of the myristoylated alanine-rich C kinase (MARCKS) protein was then determined. Despite success in analyzing fragmentation of the smaller test peptides, a unique site on the PSD for the first step of phosphorylation could not be identified because the phosphorylation reaction produced a heterogeneous mixture of products. Some molecules were phosphorylated on the serine closest to the N-terminus, and others on one of the two serines closest to the C-terminus of the peptide. Although no definitive evidence for phosphorylation on either of the remaining two serines in the PSD was found, modification there could not be ruled out by the ECD fragmentation data.
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Affiliation(s)
- Kellie A Woodling
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
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36
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He H, Conrad CA, Nilsson CL, Ji Y, Schaub TM, Marshall AG, Emmett MR. Method for lipidomic analysis: p53 expression modulation of sulfatide, ganglioside, and phospholipid composition of U87 MG glioblastoma cells. Anal Chem 2007; 79:8423-30. [PMID: 17929901 DOI: 10.1021/ac071413m] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Lipidomics can complement genomics and proteomics by providing new insight into dynamic changes in biomembranes; however, few reports in the literature have explored, on an organism-wide scale, the functional link between nonenzymatic proteins and cellular lipids. Here, we report changes induced by adenovirus-delivered wild-type p53 gene and chemotherapy of U87 MG glioblastoma cells, a treatment known to trigger apoptosis and cell cycle arrest. We compare polar lipid changes in treated cells and control cells by use of a novel, sensitive method that employs lipid extraction, one-step liquid chromatography separation, high-resolution mass analysis, and Kendrick mass defect analysis. Nano-LC FT-ICR MS and quadrupole linear ion trap MS/MS analysis of polar lipids yields hundreds of unique assignments of glyco- and phospholipids at sub-ppm mass accuracy and high resolving power (m/Deltam50% = 200 000 at m/z 400) at 1 s/scan. MS/MS data confirm molecular structures in many instances. Sulfatides are most highly modulated by wild-type p53 treatment. The treatment also leads to an increase in phospholipids such as phosphatidyl inositols, phosphatidyl serines, phosphatidyl glycerols, and phosphatidyl ethanolamines. An increase in hydroxylated phospholipids is especially noteworthy. Also, a decrease in the longer chain gangliosides, GD1 and GM1b, is observed in wild-type p53 (treated) cells.
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Affiliation(s)
- Huan He
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, USA
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37
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Sihlbom C, Wilhelmsson U, Li L, Nilsson CL, Pekny M. 14-3-3 Expression in Denervated Hippocampus after Entorhinal Cortex Lesion Assessed by Culture-Derived Isotope Tags in Quantitative Proteomics. J Proteome Res 2007; 6:3491-500. [PMID: 17663576 DOI: 10.1021/pr070108e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [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: 12/17/2022]
Abstract
Activation of astrocytes accompanies many brain pathologies. Reactive astrocytes have a beneficial role in acute neurotrauma but later on might inhibit regeneration. 2D-gel electrophoresis and mass spectrometry were applied to study the proteome difference in denervated hippocampus in wildtype mice and mice lacking intermediate filament proteins glial fibrillary acidic protein (GFAP) and vimentin (GFAP-/-Vim-/-) that show attenuated reactive gliosis and enhanced posttraumatic regeneration. Proteomic data and immunohistochemical analyses showed upregulation of the adapter protein 14-3-3 four days postlesion and suggested that 14-3-3 upregulation after injury is triggered by reactive gliosis. Culture-derived isotope tags (CDIT) and mass spectrometry demonstrated that 14-3-3 epsilon was the major isoform upregulated in denervated hippocampus and that its upregulation was attenuated in GFAP-/-Vim-/- mice and thus most likely connected to reactive gliosis.
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Affiliation(s)
- Carina Sihlbom
- Center for Brain Repair and Rehabilitation (CBR), Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Institute of Biomedicine, Sahlgrenska Academy, Göteborg University, Sweden.
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Puchades M, Nilsson CL, Emmett MR, Aldape KD, Ji Y, Lang FF, Liu TJ, Conrad CA. Proteomic investigation of glioblastoma cell lines treated with wild-type p53 and cytotoxic chemotherapy demonstrates an association between galectin-1 and p53 expression. J Proteome Res 2007; 6:869-75. [PMID: 17269744 DOI: 10.1021/pr060302l] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [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: 12/20/2022]
Abstract
Global protein analysis of treated and untreated glioblastoma cell lines was performed. Proteomic analysis revealed the identity of proteins that were significantly modulated by the treatment with wild-type TP53 and the cytotoxic chemotherapy SN38. In particular, galectin-1 was found to be negatively regulated by transfection with TP53 and further down-regulated by SN38. Expression level changes were confirmed by Western blot. Subsequent analysis of several high-grade glioma cell lines demonstrated very high levels of galectin-1, regardless if the cell lines contained mutant or wild-type TP53. High expression of galectin-1 in a human orthotopic murine tumor model was also detected by immunohistochemistry and revealed a consistent pattern of preferential expression in peripheral or leading tumor edges. Further examination of galectin-1 expression through microarray analysis in tumor materials from patients confirmed galectin-1 as a valuable biomarker and possible therapeutic target. These results demonstrate the utility of using proteomic approaches to interrogate and identify potential useful targets for cancer therapy by evaluating specific tumor responses, either positive or negative, to various therapies.
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Affiliation(s)
- Maja Puchades
- Institute of Neuroscience and Physiology, Sahlgrenska Academy, Göteborg University, SU/Mölndal, SE-43180 Mölndal, Sweden
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Nair SS, Nilsson CL, Emmett MR, Schaub TM, Gowd KH, Thakur SS, Krishnan KS, Balaram P, Marshall AG. De novo sequencing and disulfide mapping of a bromotryptophan-containing conotoxin by Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 2007; 78:8082-8. [PMID: 17134143 PMCID: PMC2518043 DOI: 10.1021/ac0607764] [Citation(s) in RCA: 43] [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] [Indexed: 11/28/2022]
Abstract
T-1-family conotoxins belong to the T-superfamily and are composed of 10-17 amino acids. They share a common cysteine framework and disulfide connectivity and exhibit unusual posttranslational modifications, such as tryptophan bromination, glutamic acid carboxylation, and threonine glycosylation. We have isolated and characterized a novel peptide, Mo1274, containing 11 amino acids, that shows the same cysteine pattern, -CC-CC, and disulfide linkage as those of the T-1-family members. The complete sequence, GNWCCSARVCC, in which W denotes bromotryptophan, was derived from MS-based de novo sequencing. The FT-ICR MS/MS techniques of electron capture dissociation (ECD), infrared multiphoton dissociation, and collision-induced dissociation served to detect and localize the tryptophan bromination. The bromine contributes a distinctive isotopic distribution in all fragments that contain bromotryptophan. ECD fragmentation results in the loss of bromine and return to the normal isotopic distribution. Disulfide connectivity of Mo1274, between cysteine pairs 1-3 and 2-4, was determined by mass spectrometry in combination with chemical derivatization employing tris(2-carboxyethyl)phosphine, followed by differential alkylation with N-ethylmaleimide and iodoacetamide. The ECD spectra of the native and partially modified peptide reveal a loss of bromine in a process that requires the presence of a disulfide bond.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Alan G. Marshall
- To whom correspondence should be addressed. Telephone: 1−850−644−0529. Fax: 1−850−644−1366. E-mail:
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40
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Carlsohn E, Nyström J, Karlsson H, Svennerholm AM, Nilsson CL. Characterization of the outer membrane protein profile from disease-related Helicobacter pylori isolates by subcellular fractionation and nano-LC FT-ICR MS analysis. J Proteome Res 2007; 5:3197-204. [PMID: 17081072 DOI: 10.1021/pr060181p] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [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: 12/16/2022]
Abstract
Because of the important role of membrane proteins in adhesion, invasion, and intracellular survival of pathogens in the host, membrane proteins are of potential interest in the search for drug targets or biomarkers. We have established a mass spectrometry-based method that allows characterization of the outer membrane protein (OMP) profile of clinical isolates from of the human gastric pathogen Helicobacter pylori. Subcellular fractionation and one-dimensional gel electrophoresis (1D-GE) analysis was combined with nano-liquid chromatography Fourier transform-ion cyclotron resonance mass spectrometry (nano-LC FT-ICR MS) and tandem mass spectrometry (MS/MS) analysis of fifteen H. pylori strains associated either with duodenal ulcers, gastric cancer, or isolated from asymptomatic H. pylori infected carriers. Over 60 unique membrane or membrane-associated proteins, including 30 of the 33 theoretically predicted OMPs, were identified from the strains. Several membrane proteins, including Omp11 and BabA, were found to be expressed by all strains. In the search for clinical markers we found that Omp26 was expressed by all disease-related strains but was only present in one out of five strains from asymptomatic carriers, which makes Omp26 a potential target for further investigation in the search for proteins unique to disease-related H. pylori strains. In addition, presence of Omp30 and absence of Omp6 seemed to be associated with H. pylori strains causing duodenal ulcer.
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Affiliation(s)
- Elisabet Carlsohn
- Institute of Biomedicine, Sahlgrenska Academy, Göteborg University, Sweden.
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41
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Marshall AG, Hendrickson CL, Emmett MR, Rodgers RP, Blakney GT, Nilsson CL. Fourier transform ion cyclotron resonance: state of the art. Eur J Mass Spectrom (Chichester) 2007; 13:57-9. [PMID: 17878540 DOI: 10.1255/ejms.846] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
This short review summarizes recent and projected advances in Fourier transform ion cyclotron resonance mass spectrometry instrumentation and applications, ranging from petroleomics to proteomics. More details are available from the cited primary literature and topical reviews.
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Affiliation(s)
- A G Marshall
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310-4005, USA
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Nilsson CL. Review: Identification of Microorganisms by Mass Spectroscopy. Anal Chem 2006. [DOI: 10.1021/ac0694728] [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: 11/30/2022]
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43
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Nair SS, Romanuka J, Billeter M, Skjeldal L, Emmett MR, Nilsson CL, Marshall AG. Structural characterization of an unusually stable cyclic peptide, kalata B2 from Oldenlandia affinis. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2006; 1764:1568-76. [PMID: 16987719 DOI: 10.1016/j.bbapap.2006.07.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 06/19/2006] [Accepted: 07/19/2006] [Indexed: 11/19/2022]
Abstract
Kalata peptides are isolated from an African medicinal plant, Oldenlandia affinis, an aqueous decoction of which can be ingested to accelerate uterine contraction during childbirth. The closely packed disulfide core of kalata peptides confers unusual stability against thermal, chemical, and enzymatic degradation. The molecular arrangement may hamper NMR-assisted disulfide connectivity assignment. We have combined NMR with high-resolution mass spectrometry (MS) and MS/MS of native and chemically derivatized kalata B2 to determine its amino acid sequence and disulfide connectivity. Infrared multiphoton dissociation establishes the disulfide bond linkages in kalata B2 as I-IV, II-V and III-VI.
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Murray S, Nilsson CL, Hare JT, Emmett MR, Korostelev A, Ongley H, Marshall AG, Chapman MS. Characterization of the capsid protein glycosylation of adeno-associated virus type 2 by high-resolution mass spectrometry. J Virol 2006; 80:6171-6. [PMID: 16731956 PMCID: PMC1472596 DOI: 10.1128/jvi.02417-05] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [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: 12/11/2022] Open
Abstract
Adeno-associated virus type 2 (AAV-2) capsid proteins have eight sequence motifs that are potential sites for O- or N-linked glycosylation. Three are in prominent surface locations, close to the sites of cellular receptor attachment and to neutralizing epitopes on or near protrusions surrounding the three-fold axes, raising the possibility that AAV-2 might use glycosylation as a means of immune escape or for preventing reattachment on release of progeny virus. Peptide mapping and structural analysis by Fourier transform ion cyclotron resonance mass spectrometry demonstrates, however, no glycosylation of the capsid protein for virus prepared in cultured HeLa cells.
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Affiliation(s)
- Sarah Murray
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA
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Abstract
Infection with the human gastric pathogen Helicobacter pylori can give rise to chronic gastritis, peptic ulcer, and gastric cancer. All H. pylori strains express the surface-localized protein HpaA, a promising candidate for a vaccine against H. pylori infection. To study the physiological importance of HpaA, a mutation of the hpaA gene was introduced into a mouse-adapted H. pylori strain. To justify that the interruption of the hpaA gene did not cause any polar effects of downstream genes or was associated with a second site mutation, the protein expression patterns of the mutant and wild-type strains were characterized by two different proteomic approaches. Two-dimensional differential in-gel electrophoresis analysis of whole-cell extracts and subcellular fractionation combined with nano-liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry for outer membrane protein profiling revealed only minor differences in the protein profile between the mutant and the wild-type strains. Therefore, the mutant strain was tested for its colonizing ability in a well-established mouse model. While inoculation with the wild-type strain resulted in heavily H. pylori-infected mice, the HpaA mutant strain was not able to establish colonization. Thus, by combining proteomic analysis and in vivo studies, we conclude that HpaA is essential for the colonization of H. pylori in mice.
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Affiliation(s)
- Elisabet Carlsohn
- Department of Medical Biochemistry, Göteborg University, Box 440, 405 30 Göteborg, Sweden.
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Sihlbom C, Davidsson P, Nilsson CL. Prefractionation of cerebrospinal fluid to enhance glycoprotein concentration prior to structural determination with FT-ICR mass spectrometry. J Proteome Res 2006; 4:2294-301. [PMID: 16335978 DOI: 10.1021/pr050210g] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [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: 11/29/2022]
Abstract
Glycoproteins in cerebrospinal fluid are found to be altered in Alzheimer patients compared to healthy control individuals. We have utilized micro-solution isoelectric focusing and affinity chromatography, prior to gel electrophoresis to enable site-specific structural determination of the N-linked glycans in apolipoprotein J with the use of FT-ICR MS. The albumin depletion method is the most suitable as prefractionation method of CSF prior to 2-DE for structural determination of glycoproteins in the study of neurodegenerative disorders.
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Affiliation(s)
- Carina Sihlbom
- Institute of Medical Biochemistry, Göteborg University, Sweden
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McFarland MA, Marshall AG, Hendrickson CL, Nilsson CL, Fredman P, Månsson JE. Structural characterization of the GM1 ganglioside by infrared multiphoton dissociation, electron capture dissociation, and electron detachment dissociation electrospray ionization FT-ICR MS/MS. J Am Soc Mass Spectrom 2005; 16:752-762. [PMID: 15862776 DOI: 10.1016/j.jasms.2005.02.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Revised: 01/31/2005] [Accepted: 02/01/2005] [Indexed: 05/24/2023]
Abstract
Gangliosides play important biological roles and structural characterization of both the carbohydrate and the lipid moieties is important. The FT-ICR MS/MS techniques of electron capture dissociation (ECD), electron detachment dissociation (EDD), and infrared multiphoton dissociation (IRMPD) provide extensive fragmentation of the protonated and deprotonated GM1 ganglioside. ECD provides extensive structural information, including identification of both halves of the ceramide and cleavage of the acetyl moiety of the N-acetylated sugars. IRMPD provides similar glycan fragmentation but no cleavage of the acetyl moiety. Cleavage between the fatty acid and the long-chain base of the ceramide moiety is seen in negative-ion IRMPD but not in positive-ion IRMPD of GM1. Furthermore, this extent of fragmentation requires a range of laser powers, whereas all information is available from a single ECD experiment. However, stepwise fragmentation by IRMPD may be used to map the relative labilities for a series of cleavages. EDD provides the alternative of electron-induced fragmentation for negative ions with extensive fragmentation, but suffers from low efficiency as well as complication of data analysis by frequent loss of hydrogen atoms. We also show that analysis of MS/MS data for glycolipids is greatly simplified by classification of product ion masses to specific regions of the ganglioside based solely on mass defect graphical analysis.
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Affiliation(s)
- Melinda A McFarland
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310-4005, USA
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Hellstrand M, Danielsen EA, Steen VM, Ekman A, Eriksson E, Nilsson CL. The ser9gly SNP in the dopamine D3 receptor causes a shift from cAMP related to PGE2 related signal transduction mechanisms in transfected CHO cells. J Med Genet 2005; 41:867-71. [PMID: 15520413 PMCID: PMC1735614 DOI: 10.1136/jmg.2004.020941] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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49
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Paulson L, Martin P, Nilsson CL, Ljung E, Westman-Brinkmalm A, Blennow K, Davidsson P. Comparative proteome analysis of thalamus in MK-801-treated rats. Proteomics 2004; 4:819-25. [PMID: 14997502 DOI: 10.1002/pmic.200300622] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [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: 11/09/2022]
Abstract
Two-dimensional gel-electrophoresis in combination with mass spectrometry is a powerful approach to compare protein expression in brain tissues. Using this proteomic approach, and based on the hypothesis that schizophrenia involves hypoglutamergic brain function, alterations in protein levels in the thalamus of rats treated with the N-methyl-D-aspartate (NMDA) receptor antagonist [+]-5-methyl-10,11-dihydro-5H-dibenzo-[a,d]-cycloheptene-5,10-iminehydrogenmaleate (MK-801), as compared to saline-treated animals, were assessed in an unbiased fashion. The rats were divided into two groups; group 1 (short-term treated) and group 2 (long-term treated). In group 1, the levels of seven proteins were increased and four proteins reduced. In group 2, the levels of six proteins were reduced. Several of the altered proteins (heat shock proteins 60 and 72, albumin, dihydropyrimidinase related protein-2, aldolase c, and malate dehydrogenase) have previously been connected to schizophrenia. Alterations of other proteins (dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex E2, guanine deaminase, alpha-enolase, aconitase, ATP-synthase and alpha-internexin), have not, to the best of our knowledge, earlier been implicated in schizophrenia pathology. Our results show the high potential of using proteomic methods for the validation of animal models of schizophrenia and to identify new proteins involved in the pathophysiological mechanisms of schizophrenia.
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Affiliation(s)
- Linda Paulson
- Departament of Clinical Neuroscience, Göteborg University, Sweden.
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50
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Puchades M, Hansson SF, Nilsson CL, Andreasen N, Blennow K, Davidsson P. Proteomic studies of potential cerebrospinal fluid protein markers for Alzheimer's disease. ACTA ACUST UNITED AC 2004; 118:140-6. [PMID: 14559363 DOI: 10.1016/j.molbrainres.2003.08.005] [Citation(s) in RCA: 221] [Impact Index Per Article: 11.1] [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: 02/06/2023]
Abstract
By comparing the cerebrospinal fluid (CSF) proteome between Alzheimer's disease (AD) patients and controls, it may be possible to identify proteins that play a role in the disease process and thus to study the pathogenesis of AD. Two-dimensional gel electrophoresis (2-DE), SYPRO Ruby staining and mass spectrometry were used for clinical screening of disease-influenced CSF proteins in AD patients compared to controls. In order to increase the detection of CSF proteins and to improve the separation of protein isoforms in a 2-D gel, micro-narrow range IPG strips were used. The levels of eight proteins and their isoforms, including apolipoprotein A1, apolipoprotein E, apolipoprotein J, beta-trace, retinol-binding protein, kininogen, alpha-1 antitrypsin, cell cycle progression 8 protein, and alpha-1beta glycoprotein were significantly altered in CSF of AD patients compared to controls. Furthermore, we also used liquid-phase IEF, as a prefractionation step, prior to 2-DE for comparison of CSF proteins between individual AD patients and controls. The levels of 37 proteins spots were altered in AD patients. One of the identified proteins, alpha-2-HS glycoprotein, has not previously been linked to AD. Our study shows that several glycoproteins are altered in AD.
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Affiliation(s)
- Maja Puchades
- Unit of Experimental Neuroscience, Department of Clinical Neuroscience, Göteborg University, Sahlgrenska University Hospital/Mölndal, S-431 80 Mölndal, Göteborg, Sweden.
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