101
|
Akande OE, Damle PK, Pop M, Sherman NE, Szomju BB, Litovchick LV, Grossman SR. DBC1 Regulates p53 Stability via Inhibition of CBP-Dependent p53 Polyubiquitination. Cell Rep 2020; 26:3323-3335.e4. [PMID: 30893604 PMCID: PMC6478392 DOI: 10.1016/j.celrep.2019.02.076] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/21/2018] [Accepted: 02/20/2019] [Indexed: 01/10/2023] Open
Abstract
The control of p53 protein stability is critical to its tumor suppressor functions. The CREB binding protein (CBP) transcriptional co-activator co-operates with MDM2 to maintain normally low physiological p53 levels in cells via exclusively cytoplasmic E4 polyubiquitination activity. Using mass spectrometry to identify nuclear and cytoplasmic CBP-interacting proteins that regulate compartmentalized CBP E4 activity, we identified deleted in breast cancer 1 (DBC1) as a stoichiometric CBP-interacting protein that negatively regulates CBP-dependent p53 polyubiquitination, stabilizes p53, and augments p53-dependent apoptosis. TCGA analysis demonstrated that solid tumors often retain wild-type p53 alleles in conjunction with DBC1 loss, supporting the hypothesis that DBC1 is selected for disruption during carcinogenesis as a surrogate for p53 functional loss. Because DBC1 maintains p53 stability in the nucleus, where p53 exerts its tumor-suppressive transcriptional function, replacement of DBC1 functionality in DBC1-deleted tumors might enhance p53 function and chemosensitivity for therapeutic benefit. Akande et al. describe DBC1 as a negative regulator of CBP p53-directed ubiquitin ligase activity that maintains nuclear p53 stability. DBC1 loss may be selected in tumors to inactivate the p53 pathway. Because expression of DBC1 enhances p53-dependent apoptosis, restoration of DBC1 in null tumors may be of therapeutic value.
Collapse
Affiliation(s)
- Oluwatoyin E Akande
- Department of Internal Medicine, Virginia Commonwealth University (VCU), Richmond, VA, USA; VCU Massey Cancer Center, VCU, Richmond, VA, USA
| | - Priyadarshan K Damle
- Department of Internal Medicine, Virginia Commonwealth University (VCU), Richmond, VA, USA; VCU Massey Cancer Center, VCU, Richmond, VA, USA
| | | | - Nicholas E Sherman
- W.M. Keck Biomedical Mass Spectrometry Laboratory, University of Virginia, Charlottesville, VA, USA
| | - Barbara B Szomju
- Department of Internal Medicine, Virginia Commonwealth University (VCU), Richmond, VA, USA; VCU Massey Cancer Center, VCU, Richmond, VA, USA
| | - Larisa V Litovchick
- Department of Internal Medicine, Virginia Commonwealth University (VCU), Richmond, VA, USA; VCU Massey Cancer Center, VCU, Richmond, VA, USA
| | - Steven R Grossman
- Department of Internal Medicine, Virginia Commonwealth University (VCU), Richmond, VA, USA; VCU Massey Cancer Center, VCU, Richmond, VA, USA.
| |
Collapse
|
102
|
Kim J. Systematic approach to characterize the dynamics of protein adsorption on the surface of biomaterials using proteomics. Colloids Surf B Biointerfaces 2020; 188:110756. [DOI: 10.1016/j.colsurfb.2019.110756] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/03/2019] [Accepted: 12/23/2019] [Indexed: 01/08/2023]
|
103
|
Kimura S, Fujisaka A, Obika S. Nucleobase derivatives induce in-source decay of oligonucleotides as new matrix-assisted laser desorption/ionization matrices. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8620. [PMID: 31658399 DOI: 10.1002/rcm.8620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE For quality control of oligonucleotide therapeutics, accurate and efficient structural characterization using mass spectrometry techniques, such as liquid chromatography/mass spectrometry (LC/MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), is essential. In MALDI MS analysis, matrix selection is critical and a new matrix could enable more efficient and rapid structural analysis. METHODS We hypothesized that nucleobase derivatives could act as matrices more efficiently than the currently used matrices for oligonucleotides because of structural similarity, which leads to close contact with the analyte. To evaluate their suitability as matrices, 16 nucleobase derivatives were selected and tested as matrix candidates for oligonucleotide analysis. RESULTS Six of the 16 nucleobase derivatives acted as matrices for oligonucleotides. Particularly, 6-thioguanine (TG) performed well and induced clear in-source decay fragmentation. When TG or 2-amino-6-chloropurine was used as the matrix, oligonucleotides were ionized, and mainly the w and d fragment ions were observed. CONCLUSIONS Herein we demonstrate that a 10-mer RNA or DNA sequence can be successfully characterized using TG as matrix and suggest the possibility of using nucleobase derivatives as novel matrices in oligonucleotide sequencing.
Collapse
Affiliation(s)
- Satoshi Kimura
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Aki Fujisaka
- Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-Kita, Tondabayashi, Osaka, 584-8540, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| |
Collapse
|
104
|
Brown KA, Tucholski T, Eken C, Knott S, Zhu Y, Jin S, Ge Y. High‐Throughput Proteomics Enabled by a Photocleavable Surfactant. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915374] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kyle A. Brown
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Trisha Tucholski
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Christian Eken
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Samantha Knott
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology University of Wisconsin-Madison Madison WI 53706 USA
| | - Song Jin
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology University of Wisconsin-Madison Madison WI 53706 USA
| |
Collapse
|
105
|
Park SG, Anderson GA, Bruce JE. Parallel Detection of Fundamental and Sixth Harmonic Signals Using an ICR Cell with Dipole and Sixth Harmonic Detectors. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:719-726. [PMID: 31967815 PMCID: PMC7970440 DOI: 10.1021/jasms.9b00144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is a powerful instrument for high-resolution analysis of biomolecules. However, relatively long signal acquisition periods are needed to achieve mass spectra with high resolution. The use of multiple detector electrodes for detection of harmonic frequencies has been introduced as one approach to increase scan rate for a given resolving power or to obtain increased resolving power for a given detection period. The achieved resolving power and scan rate increase linearly with the order of detected harmonic signals. In recent years, ICR cell geometries have been investigated to increase the order of the harmonic frequencies and enhance harmonic signal intensities. In this study, we demonstrated PCB-based ICR cell designs with dipole and sixth harmonic detectors for parallel detection of fundamental and harmonic (6f) signals. The sixth harmonic signals from the sixth harmonic detector showed an expected 6 times higher resolving power with (M + 3H)3+ charge state insulin ions as compared with that from fundamental signals from the dipole detector. Moreover, the insulin isotopic peaks with sixth harmonic frequency signals acquired with the sixth harmonic detector were resolved for a 40 ms data acquisition period but unresolved with the same duration dipole detector signals, corresponding to a 6-fold improvement in achievable spectral acquisition rates for a given resolving power.
Collapse
Affiliation(s)
- Sung-Gun Park
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Gordon A Anderson
- GAA Custom Engineering, LLC, Benton City, Washington 99320, United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| |
Collapse
|
106
|
Hale OJ, Cooper HJ. In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates. Biochem Soc Trans 2020; 48:317-326. [PMID: 32010951 PMCID: PMC7054757 DOI: 10.1042/bst20190793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 12/15/2022]
Abstract
Advances in sample preparation, ion sources and mass spectrometer technology have enabled the detection and characterisation of intact proteins. The challenges associated include an appropriately soft ionisation event, efficient transmission and detection of the often delicate macromolecules. Ambient ion sources, in particular, offer a wealth of strategies for analysis of proteins from solution environments, and directly from biological substrates. The last two decades have seen rapid development in this area. Innovations include liquid extraction surface analysis, desorption electrospray ionisation and nanospray desorption electrospray ionisation. Similarly, developments in native mass spectrometry allow protein-protein and protein-ligand complexes to be ionised and analysed. Identification and characterisation of these large ions involves a suite of hyphenated mass spectrometry techniques, often including the coupling of ion mobility spectrometry and fragmentation techniques. The latter include collision, electron and photon-induced methods, each with their own characteristics and benefits for intact protein identification. In this review, recent developments for in situ protein analysis are explored, with a focus on ion sources and tandem mass spectrometry techniques used for identification.
Collapse
Affiliation(s)
- Oliver J. Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J. Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| |
Collapse
|
107
|
Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics. Int J Mol Sci 2020; 21:ijms21041524. [PMID: 32102244 PMCID: PMC7073195 DOI: 10.3390/ijms21041524] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.
Collapse
|
108
|
Omics Approaches to Pesticide Biodegradation. Curr Microbiol 2020; 77:545-563. [DOI: 10.1007/s00284-020-01916-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/08/2020] [Indexed: 02/08/2023]
|
109
|
Li C, Attanayake K, Valentine SJ, Li P. Facile Improvement of Negative Ion Mode Electrospray Ionization Using Capillary Vibrating Sharp-Edge Spray Ionization. Anal Chem 2020; 92:2492-2502. [PMID: 31940176 PMCID: PMC7318871 DOI: 10.1021/acs.analchem.9b03983] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Electrospray ionization (ESI) is often affected by corona discharge when spraying 100% aqueous solutions as the voltage that induces discharge can be well below the onset voltage of ESI. As a result, it is especially challenging to perform native mass spectrometry in negative ion mode where 100% aqueous solution is preferred. Here we report a simple instrumentation method to improve the performance of ESI in negative ion mode based on capillary vibrating sharp-edge spray ionization. By attaching a fused silica capillary emitter to a vibrating glass slide, improved signal quality is achieved for various analytes in aqueous solutions over applying ESI alone. Compared to commercial ESI sources using nebulization gas to reduce discharge, 10-100-fold enhancement in signal intensity and 3-10-fold improvement in S/N are achieved for various kinds of molecules including DNA, peptides, proteins, and oligosaccharides. Finally, the new method demonstrates utility for native mass spectrometry analysis of proteins and G-quadruplex DNA. The present method is expected to have great potential to be adopted by the scientific community because of its improved analytical performance, simplicity, and low cost.
Collapse
Affiliation(s)
- Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| |
Collapse
|
110
|
Demichev V, Messner CB, Vernardis SI, Lilley KS, Ralser M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat Methods 2020; 17:41-44. [PMID: 31768060 PMCID: PMC6949130 DOI: 10.1038/s41592-019-0638-x] [Citation(s) in RCA: 695] [Impact Index Per Article: 173.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/09/2019] [Indexed: 01/12/2023]
Abstract
We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves the identification and quantification performance in conventional DIA proteomic applications, and is particularly beneficial for high-throughput applications, as it is fast and enables deep and confident proteome coverage when used in combination with fast chromatographic methods.
Collapse
Affiliation(s)
- Vadim Demichev
- Department of Biochemistry and The Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK
| | - Christoph B Messner
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK
| | - Spyros I Vernardis
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK
| | - Kathryn S Lilley
- Department of Biochemistry and The Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK.
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
111
|
Wang C, Wang Q, Li R, Qin J, Song L, Zhang Q, Liu M, Chen J, Wang C. LTF, PRTN3, and MNDA in Synovial Fluid as Promising Biomarkers for Periprosthetic Joint Infection: Identification by Quadrupole Orbital-Trap Mass Spectrometry. J Bone Joint Surg Am 2019; 101:2226-2234. [PMID: 31644522 DOI: 10.2106/jbjs.18.01483] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Diagnosing periprosthetic joint infection (PJI) requires various laboratory and clinical criteria. The purpose of this study was to explore novel biomarkers that could rapidly diagnose PJI with high accuracy. METHODS In this retrospective study of prospectively collected samples, 50 synovial fluid aspirates, 20 from the hip and 30 from the knee, were collected before surgery; 25 of the patients were diagnosed as having aseptic loosening (non-PJI) and 25, as having PJI according to the Musculoskeletal Infection Society criteria. A quadrupole orbital-trap mass spectrometry (MS) instrument was used to compare expression of proteins in patients with and without PJI. Proteins that were most efficacious for diagnosis of PJI were then determined using prediction analysis of microarray software and a random forest model. The most promising proteins were selected, and altered expression of these selected proteins was verified by ELISA (enzyme-linked immunosorbent assay) in an extended sample cohort. RESULTS A total of 256 proteins were significantly upregulated (≥3.0-fold) and 14 proteins were downregulated in synovial fluid of patients with PJI compared with patients without PJI. The 3 most promising proteins were lactoferrin (LTF), polymorphonuclear leukocyte serine protease 3 (PRTN3), and myeloid nuclear differentiation antigen (MNDA). When MS was used for diagnosis of PJI, the area under the curve was 0.9888 for LTF, 0.9488 for PRTN3, and 0.9632 for MNDA. ELISA results verified that LTF, MNDA, and PRTN3 were sensitive, while LTF and MNDA were specific, for diagnosis of PJI. CONCLUSIONS This proteomic study identified a previously noted protein and 2 novel candidate proteins as promising synovial fluid biomarkers for PJI diagnosis, and they should be further validated in future clinical trials. LEVEL OF EVIDENCE Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Collapse
Affiliation(s)
- Chi Wang
- Departments of Clinical Laboratory Medicine (Chi Wang, Q.W., Q.Z., and Chengbin Wang) and Orthopedics (Q.W., R.L., and J.C.), People's Liberation Army General Hospital, Beijing, People's Republic of China
| | - Qi Wang
- Departments of Clinical Laboratory Medicine (Chi Wang, Q.W., Q.Z., and Chengbin Wang) and Orthopedics (Q.W., R.L., and J.C.), People's Liberation Army General Hospital, Beijing, People's Republic of China
| | - Rui Li
- Departments of Clinical Laboratory Medicine (Chi Wang, Q.W., Q.Z., and Chengbin Wang) and Orthopedics (Q.W., R.L., and J.C.), People's Liberation Army General Hospital, Beijing, People's Republic of China
| | - Jun Qin
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center), Beijing Proteome Research Center, Beijing, People's Republic of China
| | - Lei Song
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center), Beijing Proteome Research Center, Beijing, People's Republic of China
| | - Qian Zhang
- Departments of Clinical Laboratory Medicine (Chi Wang, Q.W., Q.Z., and Chengbin Wang) and Orthopedics (Q.W., R.L., and J.C.), People's Liberation Army General Hospital, Beijing, People's Republic of China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center), Beijing Proteome Research Center, Beijing, People's Republic of China
| | - Jiying Chen
- Departments of Clinical Laboratory Medicine (Chi Wang, Q.W., Q.Z., and Chengbin Wang) and Orthopedics (Q.W., R.L., and J.C.), People's Liberation Army General Hospital, Beijing, People's Republic of China
| | - Chengbin Wang
- Departments of Clinical Laboratory Medicine (Chi Wang, Q.W., Q.Z., and Chengbin Wang) and Orthopedics (Q.W., R.L., and J.C.), People's Liberation Army General Hospital, Beijing, People's Republic of China
| |
Collapse
|
112
|
Cui Y, Yang K, Tabang DN, Huang J, Tang W, Li L. Finding the Sweet Spot in ERLIC Mobile Phase for Simultaneous Enrichment of N-Glyco and Phosphopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2491-2501. [PMID: 31286442 PMCID: PMC6917886 DOI: 10.1007/s13361-019-02230-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/10/2019] [Accepted: 04/13/2019] [Indexed: 05/30/2023]
Abstract
Simultaneous enrichment of glyco- and phosphopeptides will benefit the studies of biological processes regulated by these posttranslational modifications (PTMs). It will also reveal potential crosstalk between these two ubiquitous PTMs. Unlike custom-designed multifunctional solid phase extraction (SPE) materials, operating strong anion exchange (SAX) resin in electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) mode provides a readily available strategy to analytical labs for enrichment of these PTMs for subsequent mass spectrometry (MS)-based characterization. However, the choice of mobile phase has largely relied on empirical rules from hydrophilic interaction chromatography (HILIC) or ion-exchange chromatography (IEX) without further optimization and adjustments. In this study, ten mobile phase compositions of ERLIC were systematically compared; the impact of multiple factors including organic phase proportion, ion pairing reagent, pH, and salt on the retention of glycosylated and phosphorylated peptides was evaluated. This study demonstrated good enrichment of glyco- and phosphopeptides from the nonmodified peptides in a complex tryptic digest. Moreover, the enriched glyco- and phosphopeptides elute in different fractions by orthogonal retention mechanisms of hydrophilic interaction and electrostatic interaction in ERLIC, maximizing the LC-MS identification of each PTM. The optimized mobile phase can be adapted to the ERLIC HPLC system, where the high resolution in separating multiple PTMs will benefit large-scale MS-based PTM profiling and in-depth characterization.
Collapse
Affiliation(s)
- Yusi Cui
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Ka Yang
- School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705, USA
| | | | - Junfeng Huang
- School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705, USA
| | - Weiping Tang
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
- School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705, USA.
| |
Collapse
|
113
|
Brandi A, Piersimoni L, Feto NA, Spurio R, Alix JH, Schmidt F, Gualerzi CO. Translation initiation factor IF2 contributes to ribosome assembly and maturation during cold adaptation. Nucleic Acids Res 2019; 47:4652-4662. [PMID: 30916323 PMCID: PMC6511846 DOI: 10.1093/nar/gkz188] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/07/2019] [Accepted: 03/22/2019] [Indexed: 01/13/2023] Open
Abstract
Cold-stress in Escherichia coli induces de novo synthesis of translation initiation factors IF1, IF2 and IF3 while ribosome synthesis and assembly slow down. Consequently, the IFs/ribosome stoichiometric ratio increases about 3-fold during the first hours of cold adaptation. The IF1 and IF3 increase plays a role in translation regulation at low temperature (cold-shock-induced translational bias) but so far no specific role could be attributed to the extra copies of IF2. In this work, we show that the extra-copies of IF2 made after cold stress are associated with immature ribosomal subunits together with at least another nine proteins involved in assembly and/or maturation of ribosomal subunits. This finding, coupled with evidence that IF2 is endowed with GTPase-associated chaperone activity that promotes refolding of denatured GFP, and the finding that two cold-sensitive IF2 mutations cause the accumulation of immature ribosomal particles, indicate that IF2 is yet another GTPase protein that participates in ribosome assembly/maturation, especially at low temperatures. Overall, these findings are instrumental in redefining the functional role of IF2, which cannot be regarded as being restricted to its well documented functions in translation initiation of bacterial mRNA.
Collapse
Affiliation(s)
- Anna Brandi
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy
| | - Lolita Piersimoni
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Naser Aliye Feto
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy
| | - Roberto Spurio
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy
| | - Jean-Hervé Alix
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Claudio O Gualerzi
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy
| |
Collapse
|
114
|
Gan WZ, Ramachandran V, Lim CSY, Koh RY. Omics-based biomarkers in the diagnosis of diabetes. J Basic Clin Physiol Pharmacol 2019; 31:/j/jbcpp.ahead-of-print/jbcpp-2019-0120/jbcpp-2019-0120.xml. [PMID: 31730525 DOI: 10.1515/jbcpp-2019-0120] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023]
Abstract
Diabetes mellitus (DM) is a group of metabolic diseases related to the dysfunction of insulin, causing hyperglycaemia and life-threatening complications. Current early screening and diagnostic tests for DM are based on changes in glucose levels and autoantibody detection. This review evaluates recent studies on biomarker candidates in diagnosing type 1, type 2 and gestational DM based on omics classification, whilst highlighting the relationship of these biomarkers with the development of diabetes, diagnostic accuracy, challenges and future prospects. In addition, it also focuses on possible non-invasive biomarker candidates besides common blood biomarkers.
Collapse
Affiliation(s)
- Wei Zien Gan
- Division of Applied Biomedical Science and Biotechnology, School of Health Sciences, International Medical University, 57000 Kuala Lumpur, Malaysia
| | - Valsala Ramachandran
- Division of Applied Biomedical Science and Biotechnology, School of Health Sciences, International Medical University, 57000 Kuala Lumpur, Malaysia
| | - Crystale Siew Ying Lim
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University Kuala Lumpur, 56000 Kuala Lumpur, Malaysia
| | - Rhun Yian Koh
- Division of Applied Biomedical Science and Biotechnology, School of Health Sciences, International Medical University, 57000 Kuala Lumpur, Malaysia, Phone: +60327317207
| |
Collapse
|
115
|
Muraoka N, Sun B, Murry CE. A Proteomic Perspective on Cardiomyocyte Maturation. Circ Res 2019; 125:954-956. [PMID: 31697629 PMCID: PMC7003684 DOI: 10.1161/circresaha.119.316039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Naoto Muraoka
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
- Center for Cardiovascular Biology, University of Washington, Seattle, Washington
- Pathology University of Washington, Seattle, Washington
| | - Bingyun Sun
- Chemistry, Simon Fraser University, Burnaby, British Columbia
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
- Center for Cardiovascular Biology, University of Washington, Seattle, Washington
- Pathology University of Washington, Seattle, Washington
- Cardiology, Department of Medicine, University of Washington, Seattle, WA
- Bioengineering, University of Washington, Seattle, WA
| |
Collapse
|
116
|
Coombs KM, Simon PF, McLeish NJ, Zahedi-Amiri A, Kobasa D. Aptamer Profiling of A549 Cells Infected with Low-Pathogenicity and High-Pathogenicity Influenza Viruses. Viruses 2019; 11:v11111028. [PMID: 31694171 PMCID: PMC6893437 DOI: 10.3390/v11111028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/30/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022] Open
Abstract
Influenza A viruses (IAVs) are important animal and human emerging and re-emerging pathogens that are responsible for yearly seasonal epidemics and sporadic pandemics. IAVs cause a wide range of clinical illnesses, from relatively mild infections by seasonal strains, to acute respiratory distress during infections with highly pathogenic avian IAVs (HPAI). For this study, we infected A549 human lung cells with lab prototype A/PR/8/34 (H1N1) (PR8), a seasonal H1N1 (RV733), the 2009 pandemic H1N1 (pdm09), or with two avian strains, an H5N1 HPAI strain or an H7N9 strain that has low pathogenicity in birds but high pathogenicity in humans. We used a newly-developed aptamer-based multiplexed technique (SOMAscan®) to examine >1300 human lung cell proteins affected by the different IAV strains, and identified more than 500 significantly dysregulated cellular proteins. Our analyses indicated that the avian strains induced more profound changes in the A549 global proteome compared to all tested low-pathogenicity H1N1 strains. The PR8 strain induced a general activation, primarily by upregulating many immune molecules, the seasonal RV733 and pdm09 strains had minimal effect upon assayed molecules, and the avian strains induced significant downregulation, primarily in antimicrobial response, cardiovascular and post-translational modification systems.
Collapse
Affiliation(s)
- Kevin M. Coombs
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada (A.Z.-A.); (D.K.)
- Manitoba Centre for Proteomics & Systems Biology, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Correspondence: ; Tel.: +1-204-7893-976
| | - Philippe F. Simon
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada (A.Z.-A.); (D.K.)
- Special Pathogen Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Nigel J. McLeish
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada (A.Z.-A.); (D.K.)
| | - Ali Zahedi-Amiri
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada (A.Z.-A.); (D.K.)
- Manitoba Centre for Proteomics & Systems Biology, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Darwyn Kobasa
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada (A.Z.-A.); (D.K.)
- Special Pathogen Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| |
Collapse
|
117
|
Havlikova J, Randall EC, Griffiths RL, Swales JG, Goodwin RJA, Bunch J, Styles IB, Cooper HJ. Quantitative Imaging of Proteins in Tissue by Stable Isotope Labeled Mimetic Liquid Extraction Surface Analysis Mass Spectrometry. Anal Chem 2019; 91:14198-14202. [PMID: 31660728 PMCID: PMC7007001 DOI: 10.1021/acs.analchem.9b04148] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Absolute
quantification of proteins in tissue is important for
numerous fields of study. Liquid chromatography–mass spectrometry
(LC–MS) methods are the norm but typically involve lengthy
sample preparation including tissue homogenization, which results
in the loss of information relating to spatial distribution. Here,
we propose liquid extraction surface analysis (LESA) mass spectrometry
(MS) of stable isotope labeled mimetic tissue models for the spatially
resolved quantification of intact ubiquitin in rat and mouse brain
tissue. Measured ubiquitin concentrations are in agreement with values
found in the literature. Images of rat and mouse brain tissue demonstrate
spatial variation in the concentration of ubiquitin and demonstrate
the utility of spatially resolved quantitative measurement of proteins
in tissue. Although we have focused on ubiquitin, the method has the
potential for broader application to the absolute quantitation of
any endogenous protein or protein-based drug in tissue.
Collapse
Affiliation(s)
- Jana Havlikova
- EPSRC Centre for Doctoral Training in Physical Sciences for Health , University of Birmingham , Birmingham B15 2TT , U.K.,School of Biosciences , University of Birmingham , Birmingham B15 2TT , U.K
| | - Elizabeth C Randall
- School of Biosciences , University of Birmingham , Birmingham B15 2TT , U.K.,EPSRC Centre for Doctoral Training in Physical Sciences of Imaging in Biomedical Sciences , University of Birmingham , Birmingham B15 2TT , U.K
| | - Rian L Griffiths
- School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - John G Swales
- Pathology, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D , AstraZeneca , Cambridge CB4 0WG , U.K
| | - Richard J A Goodwin
- Pathology, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D , AstraZeneca , Cambridge CB4 0WG , U.K
| | | | - Iain B Styles
- EPSRC Centre for Doctoral Training in Physical Sciences for Health , University of Birmingham , Birmingham B15 2TT , U.K.,School of Computer Science , University of Birmingham , Birmingham B15 2TT , U.K
| | - Helen J Cooper
- School of Biosciences , University of Birmingham , Birmingham B15 2TT , U.K
| |
Collapse
|
118
|
Gomes FP, Yates JR. Recent trends of capillary electrophoresis-mass spectrometry in proteomics research. MASS SPECTROMETRY REVIEWS 2019; 38:445-460. [PMID: 31407381 PMCID: PMC6800771 DOI: 10.1002/mas.21599] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Progress in proteomics research has led to a demand for powerful analytical tools with high separation efficiency and sensitivity for confident identification and quantification of proteins, posttranslational modifications, and protein complexes expressed in cells and tissues. This demand has significantly increased interest in capillary electrophoresis-mass spectrometry (CE-MS) in the past few years. This review provides highlights of recent advances in CE-MS for proteomics research, including a short introduction to top-down mass spectrometry and native mass spectrometry (native MS), as well as a detailed overview of CE methods. Both the potential and limitations of these methods for the analysis of proteins and peptides in synthetic and biological samples and the challenges of CE methods are discussed, along with perspectives about the future direction of CE-MS. @ 2019 Wiley Periodicals, Inc. Mass Spec Rev 00:1-16, 2019.
Collapse
Affiliation(s)
| | - John R. Yates
- Correspondent author: , Phone number: (858) 784-8862, Departments of Molecular Medicine and Neurobiology, 10550 North Torrey Pines Road, SR302B, The Scripps Research Institute, La Jolla, CA 92037
| |
Collapse
|
119
|
Tian S, Siu FM, Lok CN, Fung YME, Che CM. Anticancer auranofin engages 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) as a target. Metallomics 2019; 11:1925-1936. [PMID: 31631207 DOI: 10.1039/c9mt00185a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Auranofin (AuRF) has been reported to display anticancer activity and has entered several clinical trials; however, its mechanism of action remains largely unknown. In this work, the anticancer mechanism of auranofin was investigated using a proteomics strategy entailing subcellular fractionation prior to mass spectrometric analysis. Bioinformatics analysis of the nuclear sub-proteomes revealed that tumor suppressor p14ARF is a key regulator of transcription. Through independent analysis, we validated that up-regulation of p14ARF is associated with E2F-dependent transcription and increased p53 expression. Our analyses further reveal that 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR), which is the rate-determining enzyme of the mevalonate pathway, is a novel target of auranofin with half maximal inhibitory concentration at micromolar levels. The auranofin-induced cancer cell death could be partially reverted by the addition of downstream products of the mevalonate pathway (mevalonolactone or geranyleranyl pyrophosphate (GGPP)), implying that auranofin may target the mevalonate pathway to exert its anticancer effect.
Collapse
Affiliation(s)
- Songhai Tian
- Department of Chemistry, The University of Hong Kong, Chemical Biology Centre, The Hong Kong Jockey Club Building for Interdisciplinary Research, Sassoon Road, Hong Kong SAR, China.
| | - Fung-Ming Siu
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| | - Chun-Nam Lok
- Department of Chemistry, The University of Hong Kong, Chemical Biology Centre, The Hong Kong Jockey Club Building for Interdisciplinary Research, Sassoon Road, Hong Kong SAR, China.
| | - Yi Man Eva Fung
- Department of Chemistry, The University of Hong Kong, Chemical Biology Centre, The Hong Kong Jockey Club Building for Interdisciplinary Research, Sassoon Road, Hong Kong SAR, China.
| | - Chi-Ming Che
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| |
Collapse
|
120
|
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. Mar Drugs 2019; 17:md17100576. [PMID: 31614509 PMCID: PMC6835618 DOI: 10.3390/md17100576] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
Abstract
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
Collapse
|
121
|
Samir P, Browne CM, Rahul, Sun M, Shen B, Li W, Frank J, Link AJ. Identification of Changing Ribosome Protein Compositions using Mass Spectrometry. Proteomics 2019; 18:e1800217. [PMID: 30211483 DOI: 10.1002/pmic.201800217] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/01/2018] [Indexed: 11/06/2022]
Abstract
The regulatory role of the ribosome in gene expression has come into sharper focus. It has been proposed that ribosomes are dynamic complexes capable of changing their protein composition in response to environmental stimuli. MS is applied to identify quantitative changes in the protein composition of S. cerevisiae 80S ribosomes in response to different environmental stimuli. Using quantitative MS, it is found that the paralog yeast ribosomal proteins RPL8A (eL8A) and RPL8B (eL8B) change their relative proportions in the 80S ribosome when yeast is switched from growth in glucose to glycerol. By using yeast genetics and polysome profiling, it is shown that yeast ribosomes containing either RPL8A or RPL8B are not functionally interchangeable. The quantitative proteomic data support the hypothesis that ribosomes are dynamic complexes that alter their composition and functional activity in response to changes in growth or environmental conditions.
Collapse
Affiliation(s)
- Parimal Samir
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37235, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA
| | | | - Rahul
- University of Waterloo, Waterloo, ON, Canada
| | - Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Bingxin Shen
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Wen Li
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, 10032, USA
| | - Andrew J Link
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37235, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| |
Collapse
|
122
|
Channaveerappa D, Ngounou Wetie AG, Darie CC. Bottlenecks in Proteomics: An Update. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:753-769. [PMID: 31347083 DOI: 10.1007/978-3-030-15950-4_45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Mass spectrometry (MS) is the core for advanced methods in proteomic experiments. When effectively used, proteomics may provide extensive information about proteins and their post-translational modifications, as well as their interaction partners. However, there are also many problems that one can encounter during a proteomic experiment, including, but not limited to sample preparation, sample fractionation, sample analysis, data analysis & interpretation and biological significance. Here we discuss some of the problems that researchers should be aware of when performing a proteomic experiment.
Collapse
Affiliation(s)
- Devika Channaveerappa
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Armand G Ngounou Wetie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA.
| |
Collapse
|
123
|
|
124
|
Dülfer J, Kadek A, Kopicki JD, Krichel B, Uetrecht C. Structural mass spectrometry goes viral. Adv Virus Res 2019; 105:189-238. [PMID: 31522705 DOI: 10.1016/bs.aivir.2019.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the last 20 years, mass spectrometry (MS), with its ability to analyze small sample amounts with high speed and sensitivity, has more and more entered the field of structural virology, aiming to investigate the structure and dynamics of viral proteins as close to their native environment as possible. The use of non-perturbing labels in hydrogen-deuterium exchange MS allows for the analysis of interactions between viral proteins and host cell factors as well as their dynamic responses to the environment. Cross-linking MS, on the other hand, can analyze interactions in viral protein complexes and identify virus-host interactions in cells. Native MS allows transferring viral proteins, complexes and capsids into the gas phase and has broken boundaries to overcome size limitations, so that now even the analysis of intact virions is possible. Different MS approaches not only inform about size, stability, interactions and dynamics of virus assemblies, but also bridge the gap to other biophysical techniques, providing valuable constraints for integrative structural modeling of viral complex assemblies that are often inaccessible by single technique approaches. In this review, recent advances are highlighted, clearly showing that structural MS approaches in virology are moving towards systems biology and ever more experiments are performed on cellular level.
Collapse
Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alan Kadek
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany.
| |
Collapse
|
125
|
Gaus HJ, Gupta R, Chappell AE, Østergaard ME, Swayze EE, Seth PP. Characterization of the interactions of chemically-modified therapeutic nucleic acids with plasma proteins using a fluorescence polarization assay. Nucleic Acids Res 2019; 47:1110-1122. [PMID: 30566688 PMCID: PMC6379706 DOI: 10.1093/nar/gky1260] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022] Open
Abstract
Interactions of chemically modified nucleic acid therapeutics with plasma proteins play an important role in facilitating distribution from the injection site to peripheral tissues by reducing renal clearance. Despite the importance of these interactions, analytical methods that can characterize binding constants with individual plasma proteins in a reliable and high throughput manner are not easily available. We developed a fluorescence polarization (FP) based assay and measured binding constants for the 25 most abundant human plasma proteins with phosphorothioate (PS) modified antisense oligonucleotides (ASOs). We evaluated the influence of sequence, sugar modifications, and PS content on ASO interactions with several abundant human plasma proteins and determined the effect of salt and pH on these interactions. PS ASOs were found to associate predominantly with albumin and histidine-rich glycoprotein (HRG) in mouse and human plasma by size-exclusion chromatography. In contrast, PS ASOs associate predominantly with HRG in monkey plasma because of higher concentrations of this protein in monkeys. Finally, plasma proteins capable of binding PS ASOs in human plasma were confirmed by employing affinity chromatography and proteomics. Our results indicate distinct differences in contributions from the PS backbone, nucleobase composition and oligonucleotide flexibility to protein binding.
Collapse
Affiliation(s)
- Hans J Gaus
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Ruchi Gupta
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Alfred E Chappell
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Eric E Swayze
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| |
Collapse
|
126
|
Melouane A, Ghanemi A, Yoshioka M, St-Amand J. Functional genomics applications and therapeutic implications in sarcopenia. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:175-185. [PMID: 31416575 DOI: 10.1016/j.mrrev.2019.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 03/14/2019] [Accepted: 04/17/2019] [Indexed: 12/11/2022]
Abstract
The human genome contains around 20,000-25,000 genes coding for 30,000 proteins. Some proteins and genes represent therapeutic targets for human diseases. RNA and protein expression profiling tools allow the study of the molecular basis of aging and drug discovery validation. Throughout the life, there is an age-related and disease-related muscle decline. Sarcopenia is defined as a loss of muscle mass and a decrease in functional properties such as muscle strength and physical performance. Yet, there is still no consensus on the evaluation methods of sarcopenia prognosis. The main challenge of this complex biological phenomena is its multifactorial etiology. Thus, functional genomics methods attempt to shape the related scientific approaches via an innovative in-depth view on sarcopenia. Gene and drug high throughput screening combined with functional genomics allow the generation and the interpretation of a large amount of data related to sarcopenia and therapeutic progress. This review focuses on the application of selected functional genomics techniques such as RNA interference, RNA silencing, proteomics, transgenic mice, metabolomics, genomics, and epigenomics to better understand sarcopenia mechanisms.
Collapse
Affiliation(s)
- Aicha Melouane
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, Quebec, G1V 4G2, Canada
| | - Abdelaziz Ghanemi
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, Quebec, G1V 4G2, Canada
| | - Mayumi Yoshioka
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada
| | - Jonny St-Amand
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, Quebec, G1V 4G2, Canada.
| |
Collapse
|
127
|
Xiao H, Sun F, Suttapitugsakul S, Wu R. Global and site-specific analysis of protein glycosylation in complex biological systems with Mass Spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:356-379. [PMID: 30605224 PMCID: PMC6610820 DOI: 10.1002/mas.21586] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/27/2018] [Indexed: 05/16/2023]
Abstract
Protein glycosylation is ubiquitous in biological systems and plays essential roles in many cellular events. Global and site-specific analysis of glycoproteins in complex biological samples can advance our understanding of glycoprotein functions and cellular activities. However, it is extraordinarily challenging because of the low abundance of many glycoproteins and the heterogeneity of glycan structures. The emergence of mass spectrometry (MS)-based proteomics has provided us an excellent opportunity to comprehensively study proteins and their modifications, including glycosylation. In this review, we first summarize major methods for glycopeptide/glycoprotein enrichment, followed by the chemical and enzymatic methods to generate a mass tag for glycosylation site identification. We next discuss the systematic and quantitative analysis of glycoprotein dynamics. Reversible protein glycosylation is dynamic, and systematic study of glycoprotein dynamics helps us gain insight into glycoprotein functions. The last part of this review focuses on the applications of MS-based proteomics to study glycoproteins in different biological systems, including yeasts, plants, mice, human cells, and clinical samples. Intact glycopeptide analysis is also included in this section. Because of the importance of glycoproteins in complex biological systems, the field of glycoproteomics will continue to grow in the next decade. Innovative and effective MS-based methods will exponentially advance glycoscience, and enable us to identify glycoproteins as effective biomarkers for disease detection and drug targets for disease treatment. © 2019 Wiley Periodicals, Inc. Mass Spec Rev 9999: XX-XX, 2019.
Collapse
Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| |
Collapse
|
128
|
Lualdi M, Ronci M, Zilocchi M, Corno F, Turilli ES, Sponchiado M, Aceto A, Alberio T, Fasano M. Exploring the Mitochondrial Degradome by the TAILS Proteomics Approach in a Cellular Model of Parkinson's Disease. Front Aging Neurosci 2019; 11:195. [PMID: 31417398 PMCID: PMC6685049 DOI: 10.3389/fnagi.2019.00195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/15/2019] [Indexed: 12/11/2022] Open
Abstract
Parkinson’s disease (PD) is the second most frequent neurodegenerative disease worldwide and the availability of early biomarkers and novel biotargets represents an urgent medical need. The main pathogenetic hallmark of PD is the specific loss of nigral dopaminergic neurons, in which mitochondrial dysfunction plays a crucial role. Mitochondrial proteases are central to the maintenance of healthy mitochondria and they have recently emerged as drug targets. However, an exhaustive characterization of these enzymes and their targets is still lacking, due to difficulties in analyzing proteolytic fragments by bottom-up proteomics approaches. Here, we propose the “mitochondrial dimethylation-TAILS” strategy, which combines the isolation of mitochondria with the enrichment of N-terminal peptides to analyze the mitochondrial N-terminome. We applied this method in a cellular model of altered dopamine homeostasis in neuroblastoma SH-SY5Y cells, which recapitulates early steps of PD pathogenesis. The main aim was to identify candidate mitochondrial proteases aberrantly activated by dopamine dysregulation and their cleaved targets. The proposed degradomics workflow was able to improve the identification of mitochondrial proteins if compared to classical shotgun analysis. In detail, 40% coverage of the mitochondrial proteome was obtained, the sequences of the transit peptides of two mitochondrial proteins were unveiled, and a consensus cleavage sequence for proteases involved in the processing of mitochondrial proteins was depicted. Mass spectrometry proteomics data have been submitted to ProteomeXchange with the identifier PXD013900. Moreover, sixty-one N-terminal peptides whose levels were affected by dopamine treatment were identified. By an in-depth analysis of the proteolytic peptides included in this list, eleven mitochondrial proteins showed altered proteolytic processing. One of these proteins (i.e., the 39S ribosomal protein L49 – MRPL49) was cleaved by the neprilysin protease, already exploited in clinics as a biotarget. We eventually demonstrated a mitochondrial subcellular localization of neprilysin in human cells for the first time. Collectively, these results shed new light on mitochondrial dysfunction linked to dopamine imbalance in PD and opened up the possibility to explore the mitochondrial targets of neprilysin as candidate biomarkers.
Collapse
Affiliation(s)
- Marta Lualdi
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Maurizio Ronci
- Department of Pharmacy, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Mara Zilocchi
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Federica Corno
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Emily S Turilli
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Mauro Sponchiado
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Antonio Aceto
- Department of Medical, Oral and Biotechnological Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Tiziana Alberio
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Mauro Fasano
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| |
Collapse
|
129
|
Zhang X, Lu Q, Chen C, Li X, Qing G, Sun T, Liang X. Smart polymers driven by multiple and tunable hydrogen bonds for intact phosphoprotein enrichment. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2019; 20:858-869. [PMID: 31497179 PMCID: PMC6720224 DOI: 10.1080/14686996.2019.1643259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 05/04/2023]
Abstract
Separation of phosphoproteins is essential for understanding their vital roles in biological processes and pathology. Transition metal-based receptors and antibodies, the routinely used materials for phosphoproteins enrichment, both suffer from low sensitivity, low recovery and coverage. In this work, a novel smart copolymer material was synthesized by modifying porous silica gel with a poly[(N-isopropylacrylamide-co-4-(3-acryloylthioureido) benzoic acid)0.35] (denoted as NIPAAm-co-ATBA0.35@SiO2). Driven by the hydrogen bonds complexation of ATBA monomers with phosphate groups, the copolymer-modified surface exhibited a remarkable adsorption toward native α-casein (a model phosphoprotein), accompanied with significant changes in surface viscoelasticity and roughness. Moreover, this adsorption was tunable and critically dependent on the polarity of carrier solvent. Benefiting from these features, selective enrichment of phosphoprotein was obtained using NIPAAm-co-ATBA0.35@SiO2 under a dispersive solid-phase extraction (dSPE) mode. This result displays a good potential of smart polymeric materials in phosphoprotein enrichment, which may facilitate top-down phosphoproteomics studies.
Collapse
Affiliation(s)
- Xiaofei Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Qi Lu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, P. R. China
- Research & Development Center, Jushi Group. Co., P. R. China
| | - Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, P. R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| |
Collapse
|
130
|
Cunsolo V, Foti S, Ner‐Kluza J, Drabik A, Silberring J, Muccilli V, Saletti R, Pawlak K, Harwood E, Yu F, Ciborowski P, Anczkiewicz R, Altweg K, Spoto G, Pawlaczyk A, Szynkowska MI, Smoluch M, Kwiatkowska D. Mass Spectrometry Applications. Mass Spectrom (Tokyo) 2019. [DOI: 10.1002/9781119377368.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
131
|
Cangelosi D, Resaz R, Petretto A, Segalerba D, Ognibene M, Raggi F, Mastracci L, Grillo F, Bosco MC, Varesio L, Sica A, Colombo I, Eva A. A Proteomic Analysis of GSD-1a in Mouse Livers: Evidence for Metabolic Reprogramming, Inflammation, and Macrophage Polarization. J Proteome Res 2019; 18:2965-2978. [PMID: 31173686 DOI: 10.1021/acs.jproteome.9b00309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Davide Cangelosi
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Roberta Resaz
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Andrea Petretto
- Core Facilities-Proteomics Laboratory, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Daniela Segalerba
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Marzia Ognibene
- Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Federica Raggi
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Luca Mastracci
- Department of Surgical and Diagnostic Sciences (DISC), Anatomic Pathology Unit, University of Genova, Viale Benedetto XV n. 6, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, National Cancer Research Institute, Largo Rosanna Benzi n. 10, 16132 Genova, Italy
| | - Federica Grillo
- Department of Surgical and Diagnostic Sciences (DISC), Anatomic Pathology Unit, University of Genova, Viale Benedetto XV n. 6, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, National Cancer Research Institute, Largo Rosanna Benzi n. 10, 16132 Genova, Italy
| | - Maria Carla Bosco
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Luigi Varesio
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Antonio Sica
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale “Amedeo Avogadro”, Largo Guido Donegani n. 2, 28100 Novara, Italy
- Humanitas Clinical and Research Center, Via Alessandro Manzoni n. 56, 20089 Rozzano, Italy
| | - Irma Colombo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti n. 9, 20133 Milano, Italy
| | - Alessandra Eva
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| |
Collapse
|
132
|
He Y, Mohamedali A, Huang C, Baker MS, Nice EC. Oncoproteomics: Current status and future opportunities. Clin Chim Acta 2019; 495:611-624. [PMID: 31176645 DOI: 10.1016/j.cca.2019.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023]
Abstract
Oncoproteomics is the systematic study of cancer samples using omics technologies to detect changes implicated in tumorigenesis. Recent progress in oncoproteomics is already opening new avenues for the identification of novel biomarkers for early clinical stage cancer detection, targeted molecular therapies, disease monitoring, and drug development. Such information will lead to new understandings of cancer biology and impact dramatically on the future care of cancer patients. In this review, we will summarize the advantages and limitations of the key technologies used in (onco)proteogenomics, (the Omics Pipeline), explain how they can assist us in understanding the biology behind the overarching "Hallmarks of Cancer", discuss how they can advance the development of precision/personalised medicine and the future directions in the field.
Collapse
Affiliation(s)
- Yujia He
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Abidali Mohamedali
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, New South Wales 2109, Australia
| | - Canhua Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia.
| | - Edouard C Nice
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
| |
Collapse
|
133
|
Huffman RG, Chen A, Specht H, Slavov N. DO-MS: Data-Driven Optimization of Mass Spectrometry Methods. J Proteome Res 2019; 18:2493-2500. [PMID: 31081635 DOI: 10.1021/acs.jproteome.9b00039] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The performance of ultrasensitive liquid chromatography and tandem mass spectrometry (LC-MS/MS) methods, such as single-cell proteomics by mass spectrometry (SCoPE-MS), depends on multiple interdependent parameters. This interdependence makes it challenging to specifically pinpoint the sources of problems in the LC-MS/MS methods and approaches for resolving them. For example, a low signal at the MS2 level can be due to poor LC separation, ionization, apex targeting, ion transfer, or ion detection. We sought to specifically diagnose such problems by interactively visualizing data from all levels of bottom-up LC-MS/MS analysis. Many software packages, such as MaxQuant, already provide such data, and we developed an open source platform for their interactive visualization and analysis: Data-driven Optimization of MS (DO-MS). We found that in many cases DO-MS not only specifically diagnosed LC-MS/MS problems but also enabled us to rationally optimize them. For example, by using DO-MS to optimize the sampling of the elution peak apexes, we increased ion accumulation times and apex sampling, which resulted in a 370% more efficient delivery of ions for MS2 analysis. DO-MS is easy to install and use, and its GUI allows for interactive data subsetting and high-quality figure generation. The modular design of DO-MS facilitates customization and expansion. DO-MS v1.0.8 is available for download from GitHub: https://github.com/SlavovLab/DO-MS . Additional documentation is available at https://do-ms.slavovlab.net .
Collapse
Affiliation(s)
- R Gray Huffman
- Department of Bioengineering , Northeastern University , Boston , Massachusetts 02115 , United States.,Barnett Institute , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Albert Chen
- Department of Bioengineering , Northeastern University , Boston , Massachusetts 02115 , United States.,Barnett Institute , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Harrison Specht
- Department of Bioengineering , Northeastern University , Boston , Massachusetts 02115 , United States.,Barnett Institute , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Nikolai Slavov
- Department of Bioengineering , Northeastern University , Boston , Massachusetts 02115 , United States.,Barnett Institute , Northeastern University , Boston , Massachusetts 02115 , United States.,Department of Biology , Northeastern University , Boston , Massachusetts 02115 , United States
| |
Collapse
|
134
|
Plate L, Rius B, Nguyen B, Genereux JC, Kelly JW, Wiseman RL. Quantitative Interactome Proteomics Reveals a Molecular Basis for ATF6-Dependent Regulation of a Destabilized Amyloidogenic Protein. Cell Chem Biol 2019; 26:913-925.e4. [PMID: 31105062 DOI: 10.1016/j.chembiol.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/14/2019] [Accepted: 03/31/2019] [Indexed: 12/24/2022]
Abstract
Activation of the unfolded protein response (UPR)-associated transcription factor ATF6 has emerged as a promising strategy to reduce the secretion and subsequent toxic aggregation of destabilized, amyloidogenic proteins implicated in systemic amyloid diseases. However, the molecular mechanism by which ATF6 activation reduces the secretion of amyloidogenic proteins remains poorly defined. We employ a quantitative interactomics platform to define how ATF6 activation reduces secretion of a destabilized, amyloidogenic immunoglobulin light chain (LC) associated with light-chain amyloidosis (AL). Using this platform, we show that ATF6 activation increases the targeting of this destabilized LC to a subset of pro-folding ER proteostasis factors that retains the amyloidogenic LC within the ER, preventing its secretion. Our results define a molecular basis for the ATF6-dependent reduction in destabilized LC secretion and highlight the advantage for targeting this UPR-associated transcription factor to reduce secretion of destabilized, amyloidogenic proteins implicated in AL and related systemic amyloid diseases.
Collapse
Affiliation(s)
- Lars Plate
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bibiana Rius
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA
| | - Bianca Nguyen
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA
| | - Joseph C Genereux
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA.
| |
Collapse
|
135
|
Xue Q, Beguel JP, La Peyre J. Dominin and Segon Form Multiprotein Particles in the Plasma of Eastern Oysters ( Crassostrea virginica) and Are Likely Involved in Shell Formation. Front Physiol 2019; 10:566. [PMID: 31156455 PMCID: PMC6530089 DOI: 10.3389/fphys.2019.00566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/24/2019] [Indexed: 12/14/2022] Open
Abstract
Dominin and segon are two proteins purified and characterized from the plasma of eastern oysters Crassostrea virginica, making up about 70% of the total plasma proteins. Their proposed functions are in host defense based on their pathogen binding properties and in metal metabolism based on their metal binding abilities. In the present study, the two proteins were further studied for their native states in circulation and extrapallial fluid and their possible involvement in shell formation. Two-dimensional electrophoresis confirmed that the oyster plasma was dominated by a few major proteins and size exclusion chromatography indicated that these proteins were present in circulation in a morphologically homogenous form. Density gradient ultracentrifugation in Cesium Chloride isolated morphologically homogenous particles of about 25 nm in diameter from the plasma and extrapallial fluids. Polyacrylamide gel electrophoresis identified dominin, segon and an unidentified protein as the principal components of the particles and the three proteins likely formed a multiprotein complex that associated to form the particle. Additionally, three major proteins extracted from shell organic matrix were identified based on the apparent molecular weight in SDS-PAGE to correspond to the three major proteins of plasma and protein particles. Moreover, the hemocyte expression of dominin and segon genes measured by real-time RT-PCR increased significantly upon the initiation of shell repair and were significantly greater in younger oysters. These findings suggest that dominin and segon form protein particles by association with each other and perhaps some other major plasma proteins and play a significant role in oyster shell formation.
Collapse
Affiliation(s)
- Qinggang Xue
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, Zhejiang Wanli University, Ningbo, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Jean-Philipe Beguel
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Jerome La Peyre
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| |
Collapse
|
136
|
Quantitative proteomics analysis reveals resistance differences of banana cultivar 'Brazilian' to Fusarium oxysporum f. sp. cubense races 1 and 4. J Proteomics 2019; 203:103376. [PMID: 31078632 DOI: 10.1016/j.jprot.2019.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/24/2019] [Accepted: 05/02/2019] [Indexed: 12/29/2022]
Abstract
Banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most devastating diseases in banana production. Foc is classified into three physiological races. However, the resistance mechanisms of banana against different Foc races are poorly understood. In this study, we performed a comparative proteomics analysis to investigate the resistance mechanisms of 'Brazilian' against Foc1 and Foc4. The proteomes of 'Brazilian' roots inoculated with Foc1 and Foc4 and mock inoculated control at 48 h were analyzed using TMT based quantitative analysis technique. A total of 7325 unique protein species were identified, of which 689, 744, and 1222 protein species were differentially accumulated in Foc1 vs. CK, Foc4 vs. CK, and Foc1 vs. Foc4, respectively. The differential accumulations of candidate protein species were further confirmed by RT-qPCR, PRM, and physiological and biochemical assays. Bioinformatics analysis revealed that the differentially abundance protein species (DAPS) related to pattern recognition receptors, plant cell wall modification, redox homeostasis, and defense responses were differentially accumulated after Foc1 and Foc4 infection, suggesting that 'Brazilian' differed in resistance to the two Foc races. Our study lay the foundation for an in-depth understanding of the interaction between bananas and Foc at the proteome level. SIGNIFICANCE: The banana fusarium wilt disease is one of the most destructive disease of banana and is caused by Fusarium oxysporum f. sp. cubense (Foc). Foc is classified into three physiological races, namely, Foc1, Foc2, and Foc4. Among these races, Foc1 and Foc4 are widely distributed in south China and significantly lose yield. Although both physiological races (Foc1 and Foc4) can invade the Cavendish banana cultivar 'Brazilian', they have significant pathogenicity differences. Unfortunately, how the resistance differences are produced between two races is still largely unclear to date. In this study, we addressed this issue by performing TMT-based comparative quantitative proteomics analysis of 'Brazilian' roots after inoculation with Foc1 and Foc4 as well as sterile water as the control. We revealed that the series of protein species associated with pattern recognition receptors, plant cell wall modification, redox homeostasis, pathogenesis, phytohormones and signal transduction, plant secondary metabolites and programmed cell death etc. were involved in the response to Foc infection. Notably, the potential role of lipid signaling in banana defense against Foc are not reported previously but rather unveiled for the first time in this study. The current study represents the most extensive analysis of the protein profile of 'Brazilian' in response to Foc inoculation and includes for the first time the results from comparison quantitative proteomics analysis between plants inoculated with a pathogenic strain Foc4 and a nonpathogenic strain Foc1 of 'Brazilian', which will lay the foundation for an in-depth understanding of the interaction between bananas and Foc at the proteome level.
Collapse
|
137
|
Wang T, Ma G, Ang CS, Korhonen PK, Koehler AV, Young ND, Nie S, Williamson NA, Gasser RB. High throughput LC-MS/MS-based proteomic analysis of excretory-secretory products from short-term in vitro culture of Haemonchus contortus. J Proteomics 2019; 204:103375. [PMID: 31071474 DOI: 10.1016/j.jprot.2019.05.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/08/2019] [Accepted: 05/02/2019] [Indexed: 12/27/2022]
Abstract
Parasitic nematodes of humans, animals and plants have a major, adverse impact on global health and agricultural production worldwide. To cope with their surrounding environment in and the immune attack from the host, excretory-secretory (ES) proteins are released by nematodes to orchestrate or regulate parasite-host interactions. In the present study, we characterised the ES products from short-term (12 h) in vitro culture of different developmental stages/sexes of Haemonchus contortus (one of the most important parasitic nematodes of livestock animals worldwide) using a high throughput tandem mass-spectrometry, underpinned by the most recent genomic dataset. In total, 878 unique proteins from key developmental stages/sexes (third-stage and fourth-stage larvae, and female and male adults) were identified and quantified with high confidence. Bioinformatic analyses showed noteworthy ES protein alterations during the transition from the free-living to the parasitic phase, especially for proteins which are likely involved in nutrient digestion and acquisition as well as parasite-host interactions, such as proteolytic cascade-related peptidases, glycoside hydrolases, C-type lectins and sperm-coating protein/Tpx/antigen 5/pathogenesis related-1/Sc7 (= SCP/TAPS) proteins. Our findings provide an avenue to better explore interactive processes between the host and this highly significant parasitic nematode, to underpin the search for novel drug and vaccine targets. SIGNIFICANCE: The present study represents a comprehensive proteomic analysis of the secretome of key developmental stages/sexes of H. contortus maintained in short-term in vitro culture. High throughput LC-MS/MS analysis of ES products allowed the identification of a large repertoire of proteins (secretome) and the establishment of a new proteomic database for H. contortus. The secretome of H. contortus undergoes substantial changes during the nematode's transition from free-living to parasitic stages, suggesting a constant adaptation to different environments outside of and within the host animal. Understanding the host-parasite relationship at the molecular level could assist significantly in the development of intervention strategies (i.e. novel drugs and vaccines) against H. contortus and related nematodes.
Collapse
Affiliation(s)
- Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Anson V Koehler
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Shuai Nie
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
138
|
Morsa D, Baiwir D, La Rocca R, Zimmerman TA, Hanozin E, Grifnée E, Longuespée R, Meuwis MA, Smargiasso N, Pauw ED, Mazzucchelli G. Multi-Enzymatic Limited Digestion: The Next-Generation Sequencing for Proteomics? J Proteome Res 2019; 18:2501-2513. [DOI: 10.1021/acs.jproteome.9b00044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Denis Morsa
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
- GIGA Proteomics Facility, University of Liege, Liege 4000, Belgium
| | - Dominique Baiwir
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
- GIGA Proteomics Facility, University of Liege, Liege 4000, Belgium
| | - Raphaël La Rocca
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Tyler A. Zimmerman
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Emeline Hanozin
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Elodie Grifnée
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Rémi Longuespée
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Marie-Alice Meuwis
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
- Department of Hepato-Gastroenterology and Digestive Oncology, CHU, Liege 4000, Belgium
- Laboratory of Translational Gastroenterology, GIGA, Liege 4000, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| |
Collapse
|
139
|
Presnell KV, Alper HS. Systems Metabolic Engineering Meets Machine Learning: A New Era for Data-Driven Metabolic Engineering. Biotechnol J 2019; 14:e1800416. [PMID: 30927499 DOI: 10.1002/biot.201800416] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/20/2019] [Indexed: 12/30/2022]
Abstract
The recent increase in high-throughput capacity of 'omics datasets combined with advances and interest in machine learning (ML) have created great opportunities for systems metabolic engineering. In this regard, data-driven modeling methods have become increasingly valuable to metabolic strain design. In this review, the nature of 'omics is discussed and a broad introduction to the ML algorithms combining these datasets into predictive models of metabolism and metabolic rewiring is provided. Next, this review highlights recent work in the literature that utilizes such data-driven methods to inform various metabolic engineering efforts for different classes of application including product maximization, understanding and profiling phenotypes, de novo metabolic pathway design, and creation of robust system-scale models for biotechnology. Overall, this review aims to highlight the potential and promise of using ML algorithms with metabolic engineering and systems biology related datasets.
Collapse
Affiliation(s)
- Kristin V Presnell
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24 St., Austin, TX, 78712, USA
| |
Collapse
|
140
|
Farooq QUA, Haq NU, Aziz A, Aimen S, Inam ul Haq M. Mass Spectrometry for Proteomics and Recent Developments in ESI, MALDI and other Ionization Methodologies. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164616666190204154653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background:
Mass spectrometry is a tool used in analytical chemistry to identify components
in a chemical compound and it is of tremendous importance in the field of biology for high
throughput analysis of biomolecules, among which protein is of great interest.
Objective:
Advancement in proteomics based on mass spectrometry has led the way to quantify multiple
protein complexes, and proteins interactions with DNA/RNA or other chemical compounds which
is a breakthrough in the field of bioinformatics.
Methods:
Many new technologies have been introduced in electrospray ionization (ESI) and Matrixassisted
Laser Desorption/Ionization (MALDI) techniques which have enhanced sensitivity, resolution
and many other key features for the characterization of proteins.
Results:
The advent of ambient mass spectrometry and its different versions like Desorption Electrospray
Ionization (DESI), DART and ELDI has brought a huge revolution in proteomics research.
Different imaging techniques are also introduced in MS to map proteins and other significant biomolecules.
These drastic developments have paved the way to analyze large proteins of >200kDa easily.
Conclusion:
Here, we discuss the recent advancement in mass spectrometry, which is of great importance
and it could lead us to further deep analysis of the molecules from different perspectives and
further advancement in these techniques will enable us to find better ways for prediction of molecules
and their behavioral properties.
Collapse
Affiliation(s)
- Qurat ul Ain Farooq
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
| | - Noor ul Haq
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
| | - Abdul Aziz
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
| | - Sara Aimen
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
| | - Muhammad Inam ul Haq
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
| |
Collapse
|
141
|
Metaproteomics of Freshwater Microbial Communities. Methods Mol Biol 2019. [PMID: 30980327 DOI: 10.1007/978-1-4939-9232-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recent advances in metaproteomics have provided us a link between genomic expression and functional characterization of environmental microbial communities. Therefore, the large-scale identification of proteins expressed by environmental microbiomes allows an unprecedented view of their in situ metabolism and function. However, one of the main challenges in metaproteomics remains the lack of robust analytical pipelines. This is especially true for aquatic environments with low protein concentrations and the presence of compounds that are known to interfere with traditional sample preparation pipelines and downstream LC-MS/MS analyses. In this chapter, a semiquantitative method that spans from sample preparation to functional annotation is provided. This method has been shown to provide in-depth and representative results of both the eukaryotic and prokaryotic fractions of freshwater microbiomes.
Collapse
|
142
|
An Y, Zhou L, Huang Z, Nice EC, Zhang H, Huang C. Molecular insights into cancer drug resistance from a proteomics perspective. Expert Rev Proteomics 2019; 16:413-429. [PMID: 30925852 DOI: 10.1080/14789450.2019.1601561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Resistance to chemotherapy and development of specific and effective molecular targeted therapies are major obstacles facing current cancer treatment. Comparative proteomic approaches have been employed for the discovery of putative biomarkers associated with cancer drug resistance and have yielded a number of candidate proteins, showing great promise for both novel drug target identification and personalized medicine for the treatment of drug-resistant cancer. Areas covered: Herein, we review the recent advances and challenges in proteomics studies on cancer drug resistance with an emphasis on biomarker discovery, as well as understanding the interconnectivity of proteins in disease-related signaling pathways. In addition, we highlight the critical role that post-translational modifications (PTMs) play in the mechanisms of cancer drug resistance. Expert opinion: Revealing changes in proteome profiles and the role of PTMs in drug-resistant cancer is key to deciphering the mechanisms of treatment resistance. With the development of sensitive and specific mass spectrometry (MS)-based proteomics and related technologies, it is now possible to investigate in depth potential biomarkers and the molecular mechanisms of cancer drug resistance, assisting the development of individualized therapeutic strategies for cancer patients.
Collapse
Affiliation(s)
- Yao An
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Li Zhou
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Zhao Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Edouard C Nice
- c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Canhua Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| |
Collapse
|
143
|
Chen CT, Yu JW, Ho YP. Identification of bacteria in juice/lettuce using magnetic nanoparticles and selected reaction monitoring mass spectrometry. J Food Drug Anal 2019; 27:575-584. [PMID: 30987729 PMCID: PMC9296202 DOI: 10.1016/j.jfda.2018.09.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/20/2018] [Accepted: 09/26/2018] [Indexed: 11/26/2022] Open
Abstract
Ensuring food safety requires a rapid and reliable method for detecting food-borne pathogens. Mass spectrometry has been demonstrated as a powerful tool to classify pure bacterial species. However, matrix interference from food backgrounds may lead to false results because of the suppression of microbial signals. It is useful to develop a method for bacterial enrichment and marker identification in food samples. Magnetic zirconia nanoparticles were used to concentrate spiked microorganisms from apple juice/lettuce under specific conditions (pH 4.5). Bacterial identification was achieved using nanoLC-MS. Selected reaction monitoring of bacteria-related peptides was applied for the first time to identify bacteria including Staphylococcus aureus and Escherichia coli. This study presents an accurate means for bacterial identification in food matrixes using MS. The analysis time is less than 90 min and the minimum concentration of E. coli detected was 5 × 103 CFU/mL. The interaction between bacteria and the magnetic nanoparticles was electrostatic and nonspecific, in contrast to immunoassays which require specific antibodies. The targeted peptide analysis focuses on the bacterial markers, thus significantly simplifying the analysis and leading to an accurate identification of bacteria.
Collapse
Affiliation(s)
- Cheng-Tung Chen
- Department of Chemistry, National Dong Hwa University, Hualien,
Taiwan
| | - Je-Wei Yu
- Department of Chemistry, National Dong Hwa University, Hualien,
Taiwan
| | - Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien,
Taiwan
| |
Collapse
|
144
|
Applications and challenges of forensic proteomics. Forensic Sci Int 2019; 297:350-363. [DOI: 10.1016/j.forsciint.2019.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/23/2022]
|
145
|
Sher AA, Glover KKM, Coombs KM. Zika Virus Infection Disrupts Astrocytic Proteins Involved in Synapse Control and Axon Guidance. Front Microbiol 2019; 10:596. [PMID: 30984137 PMCID: PMC6448030 DOI: 10.3389/fmicb.2019.00596] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/08/2019] [Indexed: 12/24/2022] Open
Abstract
The first human Zika virus (ZIKV) outbreak was reported in Micronesia in 2007, followed by one in Brazil in 2015. Recent studies have reported cases in Europe, Oceania and Latin America. In 2016, ZIKV transmission was also reported in the US and the World Health Organization declared it a Public Health Emergency of International Concern. Because various neurological conditions are associated with ZIKV, such as microcephaly, Guillain-Barré syndrome, and other disorders of both the central and peripheral nervous systems, including encephalopathy, (meningo)encephalitis and myelitis, and because of the lack of reliable patient diagnosis, numerous ongoing studies seek to understand molecular mechanisms underlying ZIKV pathogenesis. Astrocytes are one of the most abundant cells in the CNS. They control axonal guidance, synaptic signaling, neurotransmitter trafficking and maintenance of neurons, and are targeted by ZIKV. In this study, we used a newly developed multiplexed aptamer-based technique (SOMAScan) to examine > 1300 human astrocyte cell proteins. We identified almost 300 astrocyte proteins significantly dysregulated by ZIKV infection that span diverse functions and signaling pathways, including protein translation, synaptic control, cell migration and differentiation.
Collapse
Affiliation(s)
- Affan A Sher
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Kathleen K M Glover
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Kevin M Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| |
Collapse
|
146
|
Wang Z, Liu X, Muther J, James JA, Smith K, Wu S. Top-down Mass Spectrometry Analysis of Human Serum Autoantibody Antigen-Binding Fragments. Sci Rep 2019; 9:2345. [PMID: 30787393 PMCID: PMC6382847 DOI: 10.1038/s41598-018-38380-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/18/2018] [Indexed: 12/26/2022] Open
Abstract
Detecting autoimmune diseases at an early stage is crucial for effective treatment and disease management to slow disease progression and prevent irreversible organ damage. In many autoimmune diseases, disease-specific autoantibodies are produced by B cells in response to soluble autoantigens due to defects in B cell tolerance mechanisms. Autoantibodies accrue early in disease development, and several are so disease-specific they serve as classification criteria. In this study, we established a high-throughput, sensitive, intact serum autoantibody analysis platform based on the optimization of a one dimensional ultra-high-pressure liquid chromatography top-down mass spectrometry platform (1D UPLC-TDMS). This approach has been successfully applied to a 12 standard monoclonal antibody antigen-binding fragment (Fab) mixture, demonstrating the feasibility to separate and sequence intact antibodies with high sequence coverage and high sensitivity. We then applied the optimized platform to characterize total serum antibody Fabs in a systemic lupus erythematosus (SLE) patient sample and compared it to healthy control samples. From this analysis, we show that the SLE sample has many dominant antibody Fab-related mass features unlike the healthy controls. To our knowledge, this is the first top-down demonstration of serum autoantibody pool analysis. Our proposed approach holds great promise for discovering novel serum autoantibody biomarkers that are of interest for diagnosis, prognosis, and tolerance induction, as well as improving our understanding of pathogenic autoimmune processes.
Collapse
Affiliation(s)
- Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jennifer Muther
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Judith A James
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
| |
Collapse
|
147
|
Steinhilber AE, Schmidt FF, Naboulsi W, Planatscher H, Niedzwiecka A, Zagon J, Braeuning A, Lampen A, Joos TO, Poetz O. Application of Mass Spectrometry-Based Immunoassays for the Species- and Tissue-Specific Quantification of Banned Processed Animal Proteins in Feeds. Anal Chem 2019; 91:3902-3911. [DOI: 10.1021/acs.analchem.8b04652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andreas E. Steinhilber
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
- SIGNATOPE GmbH, Reutlingen 72770, Germany
| | - Felix F. Schmidt
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | | | | | - Alicia Niedzwiecka
- Department of Food Safety, German Federal Institute for Risk Assessment, Berlin 10589, Germany
| | - Jutta Zagon
- Department of Food Safety, German Federal Institute for Risk Assessment, Berlin 10589, Germany
| | - Albert Braeuning
- Department of Food Safety, German Federal Institute for Risk Assessment, Berlin 10589, Germany
| | - Alfonso Lampen
- Department of Food Safety, German Federal Institute for Risk Assessment, Berlin 10589, Germany
| | - Thomas O. Joos
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
- SIGNATOPE GmbH, Reutlingen 72770, Germany
| |
Collapse
|
148
|
Wang T, Ma G, Ang CS, Korhonen PK, Xu R, Nie S, Koehler AV, Simpson RJ, Greening DW, Reid GE, Williamson NA, Gasser RB. Somatic proteome of Haemonchus contortus. Int J Parasitol 2019; 49:311-320. [PMID: 30771357 DOI: 10.1016/j.ijpara.2018.12.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 12/12/2018] [Accepted: 12/17/2018] [Indexed: 01/09/2023]
Abstract
Currently, there is a dearth of proteomic data to underpin fundamental investigations of parasites and parasitism at the molecular level. Here, using a high throughput LC-MS/MS-based approach, we undertook the first reported comprehensive, large-scale proteomic investigation of the barber's pole worm (Haemonchus contortus) - one of the most important parasitic nematodes of livestock animals worldwide. In total, 2487 unique H. contortus proteins representing different developmental stages/sexes (i.e. eggs, L3s and L4s, female (Af) and male (Am) adults) were identified and quantified with high confidence. Bioinformatic analyses of this proteome revealed substantial alterations in protein profiles during the life cycle, particularly in the transition from the free-living to the parasitic phase, and key groups of proteins involved specifically in feeding, digestion, metabolism, development, parasite-host interactions (including immunomodulation), structural remodelling of the body wall and adaptive processes during parasitism. This proteomic data set will facilitate future molecular, biochemical and physiological investigations of H. contortus and related nematodes, and the discovery of novel intervention targets against haemonchosis.
Collapse
Affiliation(s)
- Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rong Xu
- Department of Biochemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria 3086, Australia
| | - Shuai Nie
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Anson V Koehler
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Richard J Simpson
- Department of Biochemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria 3086, Australia
| | - David W Greening
- Department of Biochemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria 3086, Australia
| | - Gavin E Reid
- School of Chemistry, The University of Melbourne, Parkville, Victoria 3010 Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia; Bio21 Molecular Science and Biotechnology Institute. The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
149
|
Wu Y, Wu S, Ma S, Yan F, Weng Z. Cytocompatible Modification of Thermoresponsive Polymers on Living Cells for Membrane Proteomic Isolation and Analysis. Anal Chem 2019; 91:3187-3194. [DOI: 10.1021/acs.analchem.8b04201] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yuanzi Wu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350002, China
| | - Shuigen Wu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350002, China
| | - Shanyun Ma
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350002, China
| | - Fen Yan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350002, China
| | - Zuquan Weng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350002, China
| |
Collapse
|
150
|
Glover KKM, Gao A, Zahedi-Amiri A, Coombs KM. Vero Cell Proteomic Changes Induced by Zika Virus Infection. Proteomics 2019; 19:e1800309. [PMID: 30578658 DOI: 10.1002/pmic.201800309] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/06/2018] [Indexed: 12/12/2022]
Abstract
The re-emergence and the recent spread of the Zika virus (ZIKV) has raised significant global concerns due to lack of information in patient diagnosis and management. Thus, in addition to gaining more basic information about ZIKV biology, appropriate interventions and management strategies are being sought to control ZIKV-associated diseases and its spread. This study's objective is to identify host cell proteins that are significantly dysregulated during ZIKV infection. SOMAScan, a novel aptamer-based assay, is used to simultaneously screen >1300 host proteins to detect ZIKV-induced host protein dysregulation at multiple time points during infection. A total of 125 Vero cell host proteins, including cytokines such as CXCL11 and CCL5, interferon stimulated gene 15, and translation initiation factors EIF5A and EIF4G2, are significantly dysregulated after ZIKV infection. Bioinformatic analyses of 77 host proteins, that are significantly dysregulated ≥1.25-fold, identify several activated biological processes, including the JAK/STAT, Tec kinase, and complement cascade pathways.
Collapse
Affiliation(s)
- Kathleen K M Glover
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E OJ9, Canada.,Manitoba Centre for Proteomics & Systems Biology, Winnipeg, Manitoba, R3E 3P4, Canada
| | - Ang Gao
- Manitoba Centre for Proteomics & Systems Biology, Winnipeg, Manitoba, R3E 3P4, Canada
| | - Ali Zahedi-Amiri
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E OJ9, Canada.,Manitoba Centre for Proteomics & Systems Biology, Winnipeg, Manitoba, R3E 3P4, Canada
| | - Kevin M Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E OJ9, Canada.,Manitoba Centre for Proteomics & Systems Biology, Winnipeg, Manitoba, R3E 3P4, Canada.,Children's Hospital Research Institute of Manitoba, Buhler Research Centre, Winnipeg, Manitoba, R3E 3P4, Canada
| |
Collapse
|