1
|
Alvarez-Rivera E, Ortiz-Hernández EJ, Lugo E, Lozada-Reyes LM, Boukli NM. Oncogenic Proteomics Approaches for Translational Research and HIV-Associated Malignancy Mechanisms. Proteomes 2023; 11:22. [PMID: 37489388 PMCID: PMC10366845 DOI: 10.3390/proteomes11030022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/09/2023] [Accepted: 06/29/2023] [Indexed: 07/26/2023] Open
Abstract
Recent advances in the field of proteomics have allowed extensive insights into the molecular regulations of the cell proteome. Specifically, this allows researchers to dissect a multitude of signaling arrays while targeting for the discovery of novel protein signatures. These approaches based on data mining are becoming increasingly powerful for identifying both potential disease mechanisms as well as indicators for disease progression and overall survival predictive and prognostic molecular markers for cancer. Furthermore, mass spectrometry (MS) integrations satisfy the ongoing demand for in-depth biomarker validation. For the purpose of this review, we will highlight the current developments based on MS sensitivity, to place quantitative proteomics into clinical settings and provide a perspective to integrate proteomics data for future applications in cancer precision medicine. We will also discuss malignancies associated with oncogenic viruses such as Acquire Immunodeficiency Syndrome (AIDS) and suggest novel mechanisms behind this phenomenon. Human Immunodeficiency Virus type-1 (HIV-1) proteins are known to be oncogenic per se, to induce oxidative and endoplasmic reticulum stresses, and to be released from the infected or expressing cells. HIV-1 proteins can act alone or in collaboration with other known oncoproteins, which cause the bulk of malignancies in people living with HIV-1 on ART.
Collapse
Affiliation(s)
- Eduardo Alvarez-Rivera
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | - Emanuel J. Ortiz-Hernández
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | - Elyette Lugo
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | | | - Nawal M. Boukli
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| |
Collapse
|
2
|
Bottom-Up Proteomics: Advancements in Sample Preparation. Int J Mol Sci 2023; 24:ijms24065350. [PMID: 36982423 PMCID: PMC10049050 DOI: 10.3390/ijms24065350] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist of the following three major steps: sample preparation, LC–MS/MS analysis, and data analysis. LC–MS/MS and data analysis techniques have been intensively developed, whereas sample preparation, a laborious process, remains a difficult task and the main challenge in different applications. Sample preparation is a crucial stage that affects the overall efficiency of a proteomic study; however, it is prone to errors and has low reproducibility and throughput. In-solution digestion and filter-aided sample preparation are the typical and widely used methods. In the past decade, novel methods to improve and facilitate the entire sample preparation process or integrate sample preparation and fractionation have been reported to reduce time, increase throughput, and improve reproducibility. In this review, we have outlined the current methods used for sample preparation in proteomics, including on-membrane digestion, bead-based digestion, immobilized enzymatic digestion, and suspension trapping. Additionally, we have summarized and discussed current devices and methods for integrating different steps of sample preparation and peptide fractionation.
Collapse
|
3
|
Comparative Proteomic Analysis Identifies EphA2 as a Specific Cell Surface Marker for Wharton's Jelly-Derived Mesenchymal Stem Cells. Int J Mol Sci 2020; 21:ijms21176437. [PMID: 32899389 PMCID: PMC7503404 DOI: 10.3390/ijms21176437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022] Open
Abstract
Wharton’s jelly-derived mesenchymal stem cells (WJ-MSCs) are a valuable tool in stem cell research due to their high proliferation rate, multi-lineage differentiation potential, and immunotolerance properties. However, fibroblast impurity during WJ-MSCs isolation is unavoidable because of morphological similarities and shared surface markers. Here, a proteomic approach was employed to identify specific proteins differentially expressed by WJ-MSCs in comparison to those by neonatal foreskin and adult skin fibroblasts (NFFs and ASFs, respectively). Mass spectrometry analysis identified 454 proteins with a transmembrane domain. These proteins were then compared across the different cell-lines and categorized based on their cellular localizations, biological processes, and molecular functions. The expression patterns of a selected set of proteins were further confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR), Western blotting, and immunofluorescence assays. As anticipated, most of the studied proteins had common expression patterns. However, EphA2, SLC25A4, and SOD2 were predominantly expressed by WJ-MSCs, while CDH2 and Talin2 were specific to NFFs and ASFs, respectively. Here, EphA2 was established as a potential surface-specific marker to distinguish WJ-MSCs from fibroblasts and for prospective use to prepare pure primary cultures of WJ-MSCs. Additionally, CDH2 could be used for a negative-selection isolation/depletion method to remove neonatal fibroblasts contaminating preparations of WJ-MSCs.
Collapse
|
4
|
Lin YH, Eguez RV, Torralba MG, Singh H, Golusinski P, Golusinski W, Masternak M, Nelson KE, Freire M, Yu Y. Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery. J Proteome Res 2019; 18:1907-1915. [PMID: 30848925 DOI: 10.1021/acs.jproteome.9b00037] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Clinical biomarkers identified by shotgun proteomics require proteins in body fluids or tissues to be enzymatically digested before being separated and sequenced by liquid chromatography-tandem mass spectrometry. How well peptide signals can be resolved and detected is largely dependent on the quality of sample preparation. Conventional approaches such as in-gel, in-solution, and filter-based digestion, despite their extensive implementation by the community, become less appealing due to their unsatisfying protein/peptide recovery rate, lengthy sample processing, and/or lowcost-effectiveness. Suspension trapping has recently been demonstrated as an ultrafast approach for proteomic analysis. Here, for the first time, we extend its application to human salivary proteome analyses. In particular, we present a simple self-assembled glass fiber filter device which can be packed with minimal difficulty, is extremely cost-effective, and maintains the same performance as commercial filters. As a proof-of-principle, we analyzed the whole saliva from 8 healthy individuals as well as a cohort of 10 subjects of oral squamous cell carcinoma (OSCC) patients and non-OSCC subjects. Label-free quantification revealed surprisingly low interindividual variability and several known markers. Our study provides the first evidence of an easy-to-use and low-cost device for clinical proteomics as well as for general proteomic sample preparation.
Collapse
Affiliation(s)
- Yi-Han Lin
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Rodrigo Vargas Eguez
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Manolito G Torralba
- J. Craig Venter Institute , 4120 Capricorn Lane , La Jolla , California 92037 , United States
| | - Harinder Singh
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Pawel Golusinski
- Department of Otolaryngology and Maxillofacial Surgery , University of Zielona Gora , Zielona Gora 65-417 , Poland.,Department of Head and Neck Surgery , Poznan University of Medical Sciences, Greater Poland Cancer Centre , Poznan 61-866 , Poland.,Department of Biology and Environmental Studies , Poznan University of Medical Sciences , Poznan 61-701 , Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery , Poznan University of Medical Sciences, Greater Poland Cancer Centre , Poznan 61-866 , Poland
| | - Michal Masternak
- College of Medicine, Burnett School of Biomedical Sciences , University of Central Florida , Orlando , Florida 32827 , United States
| | - Karen E Nelson
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States.,J. Craig Venter Institute , 4120 Capricorn Lane , La Jolla , California 92037 , United States
| | - Marcelo Freire
- J. Craig Venter Institute , 4120 Capricorn Lane , La Jolla , California 92037 , United States
| | - Yanbao Yu
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
| |
Collapse
|
5
|
Huang XT, Liu X, Ye CY, Tao LX, Zhou H, Zhang HY. Iron-induced energy supply deficiency and mitochondrial fragmentation in neurons. J Neurochem 2018; 147:816-830. [PMID: 30380148 DOI: 10.1111/jnc.14621] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/04/2018] [Accepted: 10/23/2018] [Indexed: 01/20/2023]
Abstract
Iron dyshomeostasis and mitochondrial impairments are both vitally important for the progression of many neurodegenerative diseases, including Parkinson's disease and Alzheimer's disease. Nevertheless, how these two pathological phenomena are linked with one another remains unclear, especially in neurons. To address the question, a model of iron overload was established with exposure of rat primary cortical neurons to excessive iron. We first verified that iron overload resulted in a decrease in adenosine triphosphate (ATP) production in neurons. Meanwhile, the release of mitochondrial cytochrome c was significantly increased after iron overload and consequently triggered an apoptosis signal, as revealed by Caspase 3 cleavage. To explore the potential underlying molecular mechanisms, an unlabeled quantitative proteomics approach was applied to primary neurons. Gene Ontology enrichment analysis revealed that 58 mitochondria-associated proteins were significantly altered, including three subunits of mitochondrial complex I and optic atrophy 1(OPA1). Increased NADH-ubiquinone oxidoreductase 75 kDa subunit and decreased NADH-ubiquinone oxidoreductase subunit A10 levels were further validated by a western blot, and more importantly, complex I activity markedly declined. Iron-induced down-regulation on the OPA1 level was also validated by a western blot, which was not reversed by the anti-oxidant but was reversed by the iron chelator. Moreover, an OPA1-associated key downstream effect, mitochondrial fragmentation, was found to be aggravated in neurons exposed to excessive iron, which is consistent with the down-regulation of OPA1. Furthermore, the protein level of PTEN-induced putative kinase 1, an important protein closely related to complex I activity and mitochondrial fragmentation, also significantly declined in neurons by iron overload. Thus, our findings may shed new light on the linkage between iron toxicity and mitochondrial impairments, such as energy supply deficiency and mitochondrial fragmentation, and further expand the toxic repertoire of iron in the central nerve system. Cover Image for this issue: doi: 10.1111/jnc.14205.
Collapse
Affiliation(s)
- Xiao Tian Huang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Xing Liu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Chun Yan Ye
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Ling Xue Tao
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Hu Zhou
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Hai Yan Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People's Republic of China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| |
Collapse
|
6
|
Zhou Y, Gao J, Zhu H, Xu J, He H, Gu L, Wang H, Chen J, Ma D, Zhou H, Zheng J. Enhancing Membrane Protein Identification Using a Simplified Centrifugation and Detergent-Based Membrane Extraction Approach. Anal Chem 2018; 90:2434-2439. [PMID: 29376338 DOI: 10.1021/acs.analchem.7b03710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane proteins may act as transporters, receptors, enzymes, and adhesion-anchors, accounting for nearly 70% of pharmaceutical drug targets. Difficulties in efficient enrichment, extraction, and solubilization still exist because of their relatively low abundance and poor solubility. A simplified membrane protein extraction approach with advantages of user-friendly sample processing procedures, good repeatability and significant effectiveness was developed in the current research for enhancing enrichment and identification of membrane proteins. This approach combining centrifugation and detergent along with LC-MS/MS successfully identified higher proportion of membrane proteins, integral proteins and transmembrane proteins in membrane fraction (76.6%, 48.1%, and 40.6%) than in total cell lysate (41.6%, 16.4%, and 13.5%), respectively. Moreover, our method tended to capture membrane proteins with high degree of hydrophobicity and number of transmembrane domains as 486 out of 2106 (23.0%) had GRAVY > 0 in membrane fraction, 488 out of 2106 (23.1%) had TMs ≥ 2. It also provided for improved identification of membrane proteins as more than 60.6% of the commonly identified membrane proteins in two cell samples were better identified in membrane fraction with higher sequence coverage. Data are available via ProteomeXchange with identifier PXD008456.
Collapse
Affiliation(s)
- Yanting Zhou
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai, China , 200237.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai, China , 201203
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai, China , 201203
| | - Hongwen Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai, China , 201203
| | - Jingjing Xu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai, China , 201203
| | - Han He
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai, China , 201203
| | - Lei Gu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai, China , 200237
| | - Hui Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai, China , 200237
| | - Jie Chen
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai, China , 201203
| | - Danjun Ma
- College of Mechanical Engineering, Dongguan University of Technology , Guangdong, China , 523808.,Qingzi Biotechnology (Shenzhen) LLC, 4026 Shen Nan Middle Road, Shenzhen, Guangdong, China , 518039
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai, China , 201203
| | - Jing Zheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai, China , 200237
| |
Collapse
|
7
|
Gao J, Zhong S, Zhou Y, He H, Peng S, Zhu Z, Liu X, Zheng J, Xu B, Zhou H. Comparative Evaluation of Small Molecular Additives and Their Effects on Peptide/Protein Identification. Anal Chem 2017; 89:5784-5792. [PMID: 28530406 DOI: 10.1021/acs.analchem.6b04886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Detergents and salts are widely used in lysis buffers to enhance protein extraction from biological samples, facilitating in-depth proteomic analysis. However, these detergents and salt additives must be efficiently removed from the digested samples prior to LC-MS/MS analysis to obtain high-quality mass spectra. Although filter-aided sample preparation (FASP), acetone precipitation (AP), followed by in-solution digestion, and strong cation exchange-based centrifugal proteomic reactors (CPRs) are commonly used for proteomic sample processing, little is known about their efficiencies at removing detergents and salt additives. In this study, we (i) developed an integrative workflow for the quantification of small molecular additives in proteomic samples, developing a multiple reaction monitoring (MRM)-based LC-MS approach for the quantification of six additives (i.e., Tris, urea, CHAPS, SDS, SDC, and Triton X-100) and (ii) systematically evaluated the relationships between the level of additive remaining in samples following sample processing and the number of peptides/proteins identified by mass spectrometry. Although FASP outperformed the other two methods, the results were complementary in terms of peptide/protein identification, as well as the GRAVY index and amino acid distributions. This is the first systematic and quantitative study of the effect of detergents and salt additives on protein identification. This MRM-based approach can be used for an unbiased evaluation of the performance of new sample preparation methods. Data are available via ProteomeXchange under identifier PXD005405.
Collapse
Affiliation(s)
- Jing Gao
- Department of Chemistry, College of Sciences, Shanghai University , Shanghai, China 200444.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Shaoyun Zhong
- Department of Chemistry, College of Sciences, Shanghai University , Shanghai, China 200444.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Yanting Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai, China 200237
| | - Han He
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Shuying Peng
- Thermo Fisher Scientific (China) Co., Ltd. , No. 6 Building, 27 Xinjinqiao Road, Shanghai, China 201206
| | - Zhenyun Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Xing Liu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Jing Zheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai, China 200237
| | - Bin Xu
- Department of Chemistry, College of Sciences, Shanghai University , Shanghai, China 200444
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203.,University of Chinese Academy of Sciences , Beijing, China 100049.,E-institute of Shanghai Municipal Education Committee, Shanghai University of Traditional Chinese Medicine , 1200 Cai Lun Road, Shanghai, China 201203
| |
Collapse
|
8
|
Herrera VLM, Steffen M, Moran AM, Tan GA, Pasion KA, Rivera K, Pappin DJ, Ruiz-Opazo N. Confirmation of translatability and functionality certifies the dual endothelin1/VEGFsp receptor (DEspR) protein. BMC Mol Biol 2016; 17:15. [PMID: 27301377 PMCID: PMC4906906 DOI: 10.1186/s12867-016-0066-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/20/2016] [Indexed: 01/16/2023] Open
Abstract
Background In contrast to rat and mouse databases, the NCBI gene database lists the human dual-endothelin1/VEGFsp receptor (DEspR, formerly Dear) as a unitary transcribed pseudogene due to a stop [TGA]-codon at codon#14 in automated DNA and RNA sequences. However, re-analysis is needed given prior single gene studies detected a tryptophan [TGG]-codon#14 by manual Sanger sequencing, demonstrated DEspR translatability and functionality, and since the demonstration of actual non-translatability through expression studies, the standard-of-excellence for pseudogene designation, has not been performed. Re-analysis must meet UNIPROT criteria for demonstration of a protein’s existence at the highest (protein) level, which a priori, would override DNA- or RNA-based deductions. Methods To dissect the nucleotide sequence discrepancy, we performed Maxam–Gilbert sequencing and reviewed 727 RNA-seq entries. To comply with the highest level multiple UNIPROT criteria for determining DEspR’s existence, we performed various experiments using multiple anti-DEspR monoclonal antibodies (mAbs) targeting distinct DEspR epitopes with one spanning the contested tryptophan [TGG]-codon#14, assessing: (a) DEspR protein expression, (b) predicted full-length protein size, (c) sequence-predicted protein-specific properties beyond codon#14: receptor glycosylation and internalization, (d) protein-partner interactions, and (e) DEspR functionality via DEspR-inhibition effects. Results Maxam–Gilbert sequencing and some RNA-seq entries demonstrate two guanines, hence a tryptophan [TGG]-codon#14 within a compression site spanning an error-prone compression sequence motif. Western blot analysis using anti-DEspR mAbs targeting distinct DEspR epitopes detect the identical glycosylated 17.5 kDa pull-down protein. Decrease in DEspR-protein size after PNGase-F digest demonstrates post-translational glycosylation, concordant with the consensus-glycosylation site beyond codon#14. Like other small single-transmembrane proteins, mass spectrometry analysis of anti-DEspR mAb pull-down proteins do not detect DEspR, but detect DEspR-protein interactions with proteins implicated in intracellular trafficking and cancer. FACS analyses also detect DEspR-protein in different human cancer stem-like cells (CSCs). DEspR-inhibition studies identify DEspR-roles in CSC survival and growth. Live cell imaging detects fluorescently-labeled anti-DEspR mAb targeted-receptor internalization, concordant with the single internalization-recognition sequence also located beyond codon#14. Conclusions Data confirm translatability of DEspR, the full-length DEspR protein beyond codon#14, and elucidate DEspR-specific functionality. Along with detection of the tryptophan [TGG]-codon#14 within an error-prone compression site, cumulative data demonstrating DEspR protein existence fulfill multiple UNIPROT criteria, thus refuting its pseudogene designation. Electronic supplementary material The online version of this article (doi:10.1186/s12867-016-0066-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Victoria L M Herrera
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Martin Steffen
- Department of Pathology and Biomedical Engineering, Boston University, Boston, USA
| | - Ann Marie Moran
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Glaiza A Tan
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Khristine A Pasion
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Keith Rivera
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Darryl J Pappin
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Nelson Ruiz-Opazo
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA. .,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.
| |
Collapse
|
9
|
Liu X, Xu Y, Meng Q, Zheng Q, Wu J, Wang C, Jia W, Figeys D, Chang Y, Zhou H. Proteomic analysis of minute amount of colonic biopsies by enteroscopy sampling. Biochem Biophys Res Commun 2016; 476:286-292. [PMID: 27230957 DOI: 10.1016/j.bbrc.2016.05.114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 05/22/2016] [Indexed: 11/26/2022]
Abstract
Colorectal cancer (CRC) is one of the most common types of malignant tumor worldwide. Currently, although many researchers have been devoting themselves in CRC studies, the process of locating biomarkers for CRC early diagnosis and prognostic is still very slow. Using a centrifugal proteomic reactor-based proteomic analysis of minute amount of colonic biopsies by enteroscopy sampling, 2620 protein groups were quantified between cancer mucosa and adjacent normal colorectal mucosa. Of which, 403 protein groups were differentially expressed with statistic significance between cancer and normal tissues, including 195 up-regulated and 208 down-regulated proteins in cancer tissues. Three proteins (SOD3, PRELP and NGAL) were selected for further Western blot validation. And the resulting Western blot experimental results were consistent with the quantitative proteomic data. SOD3 and PRELP are down-regulated in CRC mucosa comparing to adjacent normal tissue, while NGAL is up-regulated in CRC mucosa. In conclusion, the centrifugal proteomic reactor-based label-free quantitative proteomic approach provides a highly sensitive and powerful tool for analyzing minute protein sample from tiny colorectal biopsies, which may facilitate CRC biomarkers discovery for diagnoses and prognoses.
Collapse
Affiliation(s)
- Xing Liu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China
| | | | - Qian Meng
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China
| | - Qingqing Zheng
- Digestive Endoscopic Center, Shanghai Jiaotong University Affiliated Sixth People's Hospital, China
| | - Jianhong Wu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China
| | - Chen Wang
- Shanghai Key Laboratory of Diabetes Mellitus, Department of Endocrinology and Metabolism, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
| | - Weiping Jia
- Shanghai Key Laboratory of Diabetes Mellitus, Department of Endocrinology and Metabolism, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, and Department of Chemistry and Biomolecular Sciences, University of Ottawa, Canada
| | - Ying Chang
- Digestive Endoscopic Center, Shanghai Jiaotong University Affiliated Sixth People's Hospital, China.
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China.
| |
Collapse
|
10
|
Chen W, Wang S, Adhikari S, Deng Z, Wang L, Chen L, Ke M, Yang P, Tian R. Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling. Anal Chem 2016; 88:4864-71. [PMID: 27062885 DOI: 10.1021/acs.analchem.6b00631] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Great efforts have been taken for developing high-sensitive mass spectrometry (MS)-based proteomic technologies, among which sample preparation is one of the major focus. Here, a simple and integrated spintip-based proteomics technology (SISPROT) consisting of strong cation exchange beads and C18 disk in one pipet tip was developed. Both proteomics sample preparation steps, including protein preconcentration, reduction, alkylation, and digestion, and reversed phase (RP)-based desalting and high-pH RP-based peptide fractionation can be achieved in a fully integrated manner for the first time. This easy-to-use technology achieved high sensitivity with negligible sample loss. Proteomic analysis of 2000 HEK 293 cells readily identified 1270 proteins within 1.4 h of MS time, while 7826 proteins were identified when 100000 cells were processed and analyzed within only 22 h of MS time. More importantly, the SISPROT can be easily multiplexed on a standard centrifuge with good reproducibility (Pearson correlation coefficient > 0.98) for both single-shot analysis and deep proteome profiling with five-step high-pH RP fractionation. The SISPROT was exemplified by the triplicate analysis of 100000 stem cells from human exfoliated deciduous teeth (SHED). This led to the identification of 9078 proteins containing 3771 annotated membrane proteins, which was the largest proteome data set for dental stem cells reported to date. We expect that the SISPROT will be well suited for deep proteome profiling for fewer than 100000 cells and applied for translational studies where multiplexed technology with good label-free quantification precision is required.
Collapse
Affiliation(s)
- Wendong Chen
- Department of Chemistry, Fudan University , Shanghai 200433, China
| | - Shuai Wang
- ENT Institute of Shenzhen University, Shenzhen Longgang ENT Hospital , Shenzhen 518172, China
| | | | - Zuhui Deng
- ENT Institute of Shenzhen University, Shenzhen Longgang ENT Hospital , Shenzhen 518172, China
| | | | | | | | - Pengyuan Yang
- Department of Chemistry, Fudan University , Shanghai 200433, China
| | | |
Collapse
|
11
|
Shen M, Tao Y, Feng Y, Liu X, Yuan F, Zhou H. Quantitative proteomic analysis of mice corneal tissues reveals angiogenesis-related proteins involved in corneal neovascularization. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:787-93. [PMID: 27049463 DOI: 10.1016/j.bbapap.2016.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/22/2016] [Accepted: 04/01/2016] [Indexed: 01/18/2023]
Abstract
Corneal neovascularization (CNV) was induced in Balb/c mice by alkali burns in the central area of the cornea with a diameter of 2.5mm. After fourteen days, the cornea from one eye was collected for histological staining for CNV examination, while the cornea from the other eye of the same mouse was harvested for proteomic analysis. The label-free quantitative proteomic approach was applied to analyze five normal corneal tissues (normal group mice n=5) and five corresponding neovascularized corneal tissues (model group mice n=5). A total of 2124 proteins were identified, and 1682 proteins were quantified from these corneal tissues. Among these quantified proteins, 290 proteins were significantly changed between normal and alkali burned corneal tissues. Of these significantly changed proteins, 35 were reported or predicted as angiogenesis-related proteins. Then, these 35 proteins were analyzed using Ingenuity Pathway Analysis Software, resulting in 26 proteins enriched and connected to each other in the protein-protein interaction network, such as Lcn-2, αB-crystallin and Serpinf1 (PEDF). These three significantly changed proteins were selected for further Western blotting validation. Consistent with the quantitative proteomic results, Western blotting showed that Lcn-2 and αB-crystallin were significantly up-regulated in CNV model, while PEDF was down-regulated. This study provided increased understanding of angiogenesis-related proteins involved in corneal vascular development, which will be useful in the ophthalmic clinic of specifically target angiogenesis.
Collapse
Affiliation(s)
- Minqian Shen
- Department of Ophthalmology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yimin Tao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of MateriaMedica, Chinese Academy of Sciences, Shanghai 201203, China; SIMMUOMICS Laboratory, Joint Research Laboratory of Translational "OMICS" between Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China and University of Ottawa, Canada
| | - Yifan Feng
- Department of Ophthalmology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xing Liu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of MateriaMedica, Chinese Academy of Sciences, Shanghai 201203, China; SIMMUOMICS Laboratory, Joint Research Laboratory of Translational "OMICS" between Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China and University of Ottawa, Canada
| | - Fei Yuan
- Department of Ophthalmology, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of MateriaMedica, Chinese Academy of Sciences, Shanghai 201203, China; SIMMUOMICS Laboratory, Joint Research Laboratory of Translational "OMICS" between Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China and University of Ottawa, Canada.
| |
Collapse
|
12
|
Pedrazzini E, Caprera A, Fojadelli I, Stella A, Rocchetti A, Bassin B, Martinoia E, Vitale A. The Arabidopsis tonoplast is almost devoid of glycoproteins with complex N-glycans, unlike the rat lysosomal membrane. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1769-81. [PMID: 26748395 PMCID: PMC4783361 DOI: 10.1093/jxb/erv567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The distribution of the N-glycoproteome in integral membrane proteins of the vacuolar membrane (tonoplast) or the plasma membrane of Arabidopsis thaliana and, for further comparison, of the Rattus norvegicus lysosomal and plasma membranes, was analyzed. In silico analysis showed that potential N-glycosylation sites are much less frequent in tonoplast proteins. Biochemical analysis of Arabidopsis subcellular fractions with the lectin concanavalin A, which recognizes mainly unmodified N-glycans, or with antiserum against Golgi-modified N-glycans confirmed the in silico results and showed that, unlike the plant plasma membrane, the tonoplast is almost or totally devoid of N-glycoproteins with Golgi-modified glycans. Lysosomes share with vacuoles the hydrolytic functions and the position along the secretory pathway; however, our results indicate that their membranes had a divergent evolution. We propose that protection against the luminal hydrolases that are abundant in inner hydrolytic compartments, which seems to have been achieved in many lysosomal membrane proteins by extensive N-glycosylation of the luminal domains, has instead been obtained in the vast majority of tonoplast proteins by limiting the length of such domains.
Collapse
Affiliation(s)
| | | | | | | | | | - Barbara Bassin
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Enrico Martinoia
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | | |
Collapse
|
13
|
Xu J, Gao J, Yu C, He H, Yang Y, Figeys D, Zhou H. Development of Online pH Gradient-Eluted Strong Cation Exchange Nanoelectrospray-Tandem Mass Spectrometry for Proteomic Analysis Facilitating Basic and Histidine-Containing Peptides Identification. Anal Chem 2015; 88:583-91. [DOI: 10.1021/acs.analchem.5b04000] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jingjing Xu
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Gao
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- SIMMUOMICS
Laboratory, Joint Research Laboratory of Translational “OMICS” between Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China and University of Ottawa, Canada, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Chengli Yu
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Han He
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Yiming Yang
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Daniel Figeys
- Department
of Biochemistry, Microbiology and Immunology, and Department of Chemistry
and Biomolecular Sciences, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- SIMMUOMICS
Laboratory, Joint Research Laboratory of Translational “OMICS” between Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China and University of Ottawa, Canada, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Hu Zhou
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- SIMMUOMICS
Laboratory, Joint Research Laboratory of Translational “OMICS” between Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China and University of Ottawa, Canada, 555 Zuchongzhi Road, Shanghai, 201203, China
| |
Collapse
|
14
|
Ye X, Zhang Y, He B, Meng Y, Li Y, Gao Y. Quantitative proteomic analysis identifies new effectors of FOXM1 involved in breast cancer cell migration. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:15836-15844. [PMID: 26884854 PMCID: PMC4730067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/22/2015] [Indexed: 06/05/2023]
Abstract
The Forkhead Box M1 (FOXM1) transcription factor plays important roles in tumorigenesis and tumor metastasis in multiple human carcinomas. However, the underlying mechanisms for FOXM1 function remain to be classified. In the present study, we employed quantitative proteomic approach to search new downstream targets of FOXM1 in breast cancer MDA-MB-231 cells. A total of 4125 proteins were identified and quantified by label-free quantitation, of which 318 proteins were significantly changed (with P-value <0.05) between FOXM1 knockdown cells and control cells. Among them, three proteins ACSL4, CGGBP1 and PGRMC2 were significantly downregulated with FOXM1 reduction by western blot analysis. Further functional assays revealed that knockdown of the three proteins in MDA-MB-231 cells attenuated the ability of cell migration, consistent with the phenotype of FOXM1 knockdown. These results suggest that new potential downstream effectors of FOXM1 were identified by proteomic approach, and may provide new potential therapeutic targets in breast cancer.
Collapse
Affiliation(s)
- Xiaojuan Ye
- Department of Oncology, East Hospital, Tongji University School of MedicineShanghai 200120, China
| | - Yi Zhang
- Department of Oncology, East Hospital, Dalian Medical UniversityShanghai 200120, China
| | - Bin He
- Research Center for Translational Medicine, East Hospital, Tongji University School of MedicineShanghai 200120, China
| | - Yuesheng Meng
- Department of Oncology, East Hospital, Tongji University School of MedicineShanghai 200120, China
| | - Yandong Li
- Department of Oncology, East Hospital, Tongji University School of MedicineShanghai 200120, China
| | - Yong Gao
- Department of Oncology, East Hospital, Tongji University School of MedicineShanghai 200120, China
| |
Collapse
|
15
|
Liu C, Choi K, Kang Y, Kim J, Fobel C, Seale B, Campbell JL, Covey TR, Wheeler AR. Direct Interface between Digital Microfluidics and High Performance Liquid Chromatography-Mass Spectrometry. Anal Chem 2015; 87:11967-72. [PMID: 26595766 DOI: 10.1021/acs.analchem.5b03616] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We introduce an automated method to facilitate in-line coupling of digital microfluidics (DMF) with HPLC-MS, using a custom, 3D-printed manifold and a custom plugin to the popular open-source control system, DropBot. The method was designed to interface directly with commercial autosamplers (with no prior modification), suggesting that it will be widely accessible for end-users. The system was demonstrated to be compatible with samples dissolved in aqueous buffers and neat methanol and was validated by application to a common steroid-labeling derivatization reaction. We propose that the methods described here will be useful for a wide range of applications, combining the automated sample processing power of DMF with the resolving and analytical capacity of HPLC-MS.
Collapse
Affiliation(s)
- Chang Liu
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.,SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Kihwan Choi
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Yang Kang
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Jihye Kim
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Christian Fobel
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Brendon Seale
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | | | - Thomas R Covey
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto , 164 College Street, Toronto, Ontario M5S 3G9, Canada.,Donnelly Centre for Cellular and Biomolecular Research, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| |
Collapse
|
16
|
Fang X, Qiao L, Yan G, Yang P, Liu B. Multifunctional nanoreactor for comprehensive characterization of membrane proteins based on surface functionalized mesoporous foams. Anal Chem 2015; 87:9360-7. [PMID: 26305297 DOI: 10.1021/acs.analchem.5b02135] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An integrated protocol is proposed here for efficient analysis of membrane proteins based on surface functionalized mesoporous graphene foams (MGF). The inherent hydrophobic nature of MGF and surface modification with hydrophilic chitosan (CS) make it highly suitable for the enrichment of hydrophobic membrane proteins from organic solvent, while remaining well-dispersed in aqueous solution for subsequent proteolysis. Therefore, such a multifunctional reactor ensures a facile solvent adjustment route. Furthermore, as a chitosan modified nanoporous reactor, it also provides a biocompatible nanoenvironment that can maintain the stability and activity of enzymes to realize efficient in situ digestion of the enriched membrane proteins. The concept was first proved with a standard hydrophobic membrane protein, bacteriorhodopsin, where a high number of identified peptides and amino acid sequence coverage were achieved even at extremely low protein concentration. The mesoporous reaction system was further applied to the analysis of complex real-case proteome samples, where 931 membrane proteins were identified in triplicate analyses by 2D LC-MS/MS. In contrast, with in-solution proteolysis, only 73 membrane proteins were identified from the same sample by the same 2D LC-MS/MS. The identified membrane proteins by the MGF-CS protocol include many biomarkers of the cell line. These results suggest that the multifunctional MGF-CS protocol is of great value to facilitate the comprehensive characterization of membrane proteins in the proteome research.
Collapse
Affiliation(s)
- Xiaoni Fang
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Liang Qiao
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Guoquan Yan
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Baohong Liu
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| |
Collapse
|
17
|
The proteomic landscape of the suprachiasmatic nucleus clock reveals large-scale coordination of key biological processes. PLoS Genet 2014; 10:e1004695. [PMID: 25330117 PMCID: PMC4199512 DOI: 10.1371/journal.pgen.1004695] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/21/2014] [Indexed: 11/19/2022] Open
Abstract
The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry. Of the 2112 proteins that were accurately quantified, 20% (421 proteins) displayed a time-of-day-dependent expression profile. Within this time-of-day proteome, 11% (48 proteins) were further defined as circadian based on a sinusoidal expression pattern with a ∼24 h period. Nine circadianly expressed proteins exhibited 24 h rhythms at the transcript level, with an average time lag that exceeded 8 h. A substantial proportion of the time-of-day proteome exhibited abrupt fluctuations at the anticipated light-to-dark and dark-to-light transitions, and was enriched for proteins involved in several key biological pathways, most notably, mitochondrial oxidative phosphorylation. Additionally, predicted targets of miR-133ab were enriched in specific hierarchical clusters and were inversely correlated with miR133ab expression in the SCN. These insights into the proteomic landscape of the SCN will facilitate a more integrative understanding of cellular control within the SCN clock. The suprachiasmatic nucleus (SCN) serves as the master circadian pacemaker in mammals, coordinating the physiological responses of a myriad of peripheral clocks throughout the body and linking their rhythms to the environmental light-dark cycle. In this study, we interrogated the murine SCN proteome across the circadian cycle using stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative mass spectrometry. Among 3275 identified proteins in the SCN, 421 displayed a time-of-day-dependent expression profile, 48 fit a circadian expression profile with a ∼24 h period, and a surprising number of proteins were ultradianly expressed. Nine circadianly expressed proteins were accompanied by transcripts that were also 24 h rhythmic, but with a significant time lag (>8 h) between the phases of peak mRNA vs. protein expression. A substantial proportion of the time-of-day proteome exhibited abrupt fluctuations at the anticipated dawn and dusk, and was involved in mitochondrial oxidative phosphorylation. Additionally, predicted targets of miR-133ab were enriched in specific hierarchical clusters and were inversely correlated with miR133ab expression in the SCN. Our study underscores the significance of post-transcriptional regulation, the surprising prevalence of ultradian protein expression, and the functional implications on mitochondrial energy metabolism.
Collapse
|
18
|
Tian R. Exploring intercellular signaling by proteomic approaches. Proteomics 2013; 14:498-512. [DOI: 10.1002/pmic.201300259] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/15/2013] [Accepted: 08/28/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Ruijun Tian
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Toronto ON Canada
| |
Collapse
|
19
|
Abu-Farha M, Tiss A, Abubaker J, Khadir A, Al-Ghimlas F, Al-Khairi I, Baturcam E, Cherian P, Elkum N, Hammad M, John J, Kavalakatt S, Warsame S, Behbehani K, Dermime S, Dehbi M. Proteomics analysis of human obesity reveals the epigenetic factor HDAC4 as a potential target for obesity. PLoS One 2013; 8:e75342. [PMID: 24086512 PMCID: PMC3782461 DOI: 10.1371/journal.pone.0075342] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/13/2013] [Indexed: 02/07/2023] Open
Abstract
Sedentary lifestyle and excessive energy intake are prominent contributors to obesity; a major risk factors for the development of insulin resistance, type 2 diabetes and cardiovascular diseases. Elucidating the molecular mechanisms underlying these chronic conditions is of relevant importance as it might lead to the identification of novel anti-obesity targets. The purpose of the current study is to investigate differentially expressed proteins between lean and obese subjects through a shot-gun quantitative proteomics approach using peripheral blood mononuclear cells (PBMCs) extracts as well as potential modulation of those proteins by physical exercise. Using this approach, a total of 47 proteins showed at least 1.5 fold change between lean and obese subjects. In obese, the proteomic profiling before and after 3 months of physical exercise showed differential expression of 38 proteins. Thrombospondin 1 (TSP1) was among the proteins that were upregulated in obese subjects and then decreased by physical exercise. Conversely, the histone deacetylase 4 (HDAC4) was downregulated in obese subjects and then induced by physical exercise. The proteomic data was further validated by qRT-PCR, Western blot and immunohistochemistry in both PBMCs and adipose tissue. We also showed that HDAC4 levels correlated positively with maximum oxygen consumption (VO2 Max) but negatively with body mass index, percent body fat, and the inflammatory chemokine RANTES. In functional assays, our data indicated that ectopic expression of HDAC4 significantly impaired TNF-α-dependent activation of NF-κB, establishing thus a link between HDAC4 and regulation of the immune system. Together, the expression pattern of HDAC4 in obese subjects before and after physical exercise, its correlation with various physical, clinical and metabolic parameters along with its inhibitory effect on NF-κB are suggestive of a protective role of HDAC4 against obesity. HDAC4 could therefore represent a potential therapeutic target for the control and management of obesity and presumably insulin resistance.
Collapse
Affiliation(s)
- Mohamed Abu-Farha
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Ali Tiss
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Jehad Abubaker
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Abdelkrim Khadir
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Fahad Al-Ghimlas
- Fitness and Rehabilitation Centre, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Irina Al-Khairi
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Engin Baturcam
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Preethi Cherian
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Naser Elkum
- Department of Biostatistics & Epidemiology, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Maha Hammad
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Jeena John
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Sina Kavalakatt
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Samia Warsame
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Kazem Behbehani
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
- Fitness and Rehabilitation Centre, Dasman Diabetes Institute, Kuwait, Kuwait
- Department of Biostatistics & Epidemiology, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Said Dermime
- Biomedical Research Facility, King Fahad Specialist Hospital Dammam, Dammam, Kingdom of Saudi Arabia
| | - Mohammed Dehbi
- Department of Biomedical Research, Dasman Diabetes Institute, Kuwait, Kuwait
- Genomic Medicine and Systems Biology Research Center, Qatar Biomedical Research Institute, Education City, Doha, Qatar
| |
Collapse
|
20
|
Zhao Q, Liang Y, Yuan H, Sui Z, Wu Q, Liang Z, Zhang L, Zhang Y. Biphasic Microreactor for Efficient Membrane Protein Pretreatment with a Combination of Formic Acid Assisted Solubilization, On-Column pH Adjustment, Reduction, Alkylation, and Tryptic Digestion. Anal Chem 2013; 85:8507-12. [DOI: 10.1021/ac402076u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Qun Zhao
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yu Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Huiming Yuan
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Zhigang Sui
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Qi Wu
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Lihua Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yukui Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| |
Collapse
|
21
|
Ma Y, Yang C, Tao Y, Zhou H, Wang Y. Recent technological developments in proteomics shed new light on translational research on diabetic microangiopathy. FEBS J 2013; 280:5668-81. [PMID: 23763694 DOI: 10.1111/febs.12369] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/27/2013] [Accepted: 05/30/2013] [Indexed: 12/23/2022]
Abstract
Diabetic microangiopathy has become a heavy social burden worldwide, but at present it is still difficult to predict and diagnose this ailment at an early stage. Various proteomics approaches have been applied to the pathophysiological study of diabetic microangiopathy. Conventional proteomics methods, including gel-based methods, exhibit limited sensitivity and robustness and have typically been used in high- or middle-abundance biomarker discovery. Clinical samples from patients with diabetic microangiopathy, such as biopsy samples, are minute in size. Therefore sample preparation, quantitative labelling and mass spectrometry technologies need to be optimized for low-abundance protein detection, multiple-sample processing and precision quantitation. In this review, we briefly introduce the recent technological developments in proteomics methods and summarize current proteomics-based, translational research on diabetic microangiopathy. Recent technological developments in proteomics tools may shed new light on the pathogenesis of diabetic microangiopathy and biomarkers and therapeutic targets related to this condition.
Collapse
Affiliation(s)
- Yuhang Ma
- Department of Endocrinology and Metabolism, Shanghai First People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | | | | | | | | |
Collapse
|
22
|
Pham MD, Yu SSF, Han CC, Chan SI. Improved Mass Spectrometric Analysis of Membrane Proteins Based on Rapid and Versatile Sample Preparation on Nanodiamond Particles. Anal Chem 2013; 85:6748-55. [DOI: 10.1021/ac400713g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Minh D. Pham
- Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Steve S.-F. Yu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chau-Chung Han
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Sunney I. Chan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| |
Collapse
|
23
|
Fowler S, Akins M, Zhou H, Figeys D, Bennett SA. The liver connexin32 interactome is a novel plasma membrane-mitochondrial signaling nexus. J Proteome Res 2013; 12:2597-610. [PMID: 23590695 PMCID: PMC3714164 DOI: 10.1021/pr301166p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Indexed: 02/07/2023]
Abstract
Connexins are the structural subunits of gap junctions and act as protein platforms for signaling complexes. Little is known about tissue-specific connexin signaling nexuses, given significant challenges associated with affinity-purifying endogenous channel complexes to the level required for interaction analyses. Here, we used multiple subcellular fractionation techniques to isolate connexin32-enriched membrane microdomains from murine liver. We show, for the first time, that connexin32 localizes to both the plasma membrane and inner mitochondrial membrane of hepatocytes. Using a combination of immunoprecipitation-high throughput mass spectrometry, reciprocal co-IP, and subcellular fractionation methodologies, we report a novel interactome validated using null mutant controls. Eighteen connexin32 interacting proteins were identified. The majority represent resident mitochondrial proteins, a minority represent plasma membrane, endoplasmic reticulum, or cytoplasmic partners. In particular, connexin32 interacts with connexin26 and the mitochondrial protein, sideroflexin-1, at the plasma membrane. Connexin32 interaction enhances connexin26 stability. Converging bioinformatic, biochemical, and confocal analyses support a role for connexin32 in transiently tethering mitochondria to connexin32-enriched plasma membrane microdomains through interaction with proteins in the outer mitochondrial membrane, including sideroflexin-1. Complex formation increases the pool of sideroflexin-1 that is present at the plasma membrane. Together, these data identify a novel plasma membrane/mitochondrial signaling nexus in the connexin32 interactome.
Collapse
Affiliation(s)
- Stephanie
L. Fowler
- Neural
Regeneration Laboratory, Ottawa Institute of Systems Biology, Department of
Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Mark Akins
- Neural
Regeneration Laboratory, Ottawa Institute of Systems Biology, Department of
Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Hu Zhou
- Neural
Regeneration Laboratory, Ottawa Institute of Systems Biology, Department of
Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai,
China
| | - Daniel Figeys
- Neural
Regeneration Laboratory, Ottawa Institute of Systems Biology, Department of
Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Steffany A.L. Bennett
- Neural
Regeneration Laboratory, Ottawa Institute of Systems Biology, Department of
Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
24
|
Tao Y, Fang L, Yang Y, Jiang H, Yang H, Zhang H, Zhou H. Quantitative proteomic analysis reveals the neuroprotective effects of huperzine A for amyloid beta treated neuroblastoma N2a cells. Proteomics 2013; 13:1314-24. [DOI: 10.1002/pmic.201200437] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 11/25/2012] [Accepted: 11/26/2012] [Indexed: 02/04/2023]
Affiliation(s)
| | | | | | - Hualiang Jiang
- Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai; China
| | - Huaiyu Yang
- Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai; China
| | | | | |
Collapse
|
25
|
Vuckovic D, Dagley LF, Purcell AW, Emili A. Membrane proteomics by high performance liquid chromatography-tandem mass spectrometry: Analytical approaches and challenges. Proteomics 2013; 13:404-23. [DOI: 10.1002/pmic.201200340] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/24/2012] [Accepted: 10/09/2012] [Indexed: 01/01/2023]
Affiliation(s)
- Dajana Vuckovic
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto ON Canada
| | - Laura F. Dagley
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto ON Canada
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Victoria Australia
| | - Andrew Emili
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto ON Canada
- Department of Molecular Genetics; University of Toronto; Toronto ON Canada
| |
Collapse
|
26
|
Neveu G, Barouch-Bentov R, Ziv-Av A, Gerber D, Jacob Y, Einav S. Identification and targeting of an interaction between a tyrosine motif within hepatitis C virus core protein and AP2M1 essential for viral assembly. PLoS Pathog 2012; 8:e1002845. [PMID: 22916011 PMCID: PMC3420927 DOI: 10.1371/journal.ppat.1002845] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/24/2012] [Indexed: 12/24/2022] Open
Abstract
Novel therapies are urgently needed against hepatitis C virus infection (HCV), a major global health problem. The current model of infectious virus production suggests that HCV virions are assembled on or near the surface of lipid droplets, acquire their envelope at the ER, and egress through the secretory pathway. The mechanisms of HCV assembly and particularly the role of viral-host protein-protein interactions in mediating this process are, however, poorly understood. We identified a conserved heretofore unrecognized YXXΦ motif (Φ is a bulky hydrophobic residue) within the core protein. This motif is homologous to sorting signals within host cargo proteins known to mediate binding of AP2M1, the μ subunit of clathrin adaptor protein complex 2 (AP-2), and intracellular trafficking. Using microfluidics affinity analysis, protein-fragment complementation assays, and co-immunoprecipitations in infected cells, we show that this motif mediates core binding to AP2M1. YXXΦ mutations, silencing AP2M1 expression or overexpressing a dominant negative AP2M1 mutant had no effect on HCV RNA replication, however, they dramatically inhibited intra- and extracellular infectivity, consistent with a defect in viral assembly. Quantitative confocal immunofluorescence analysis revealed that core's YXXΦ motif mediates recruitment of AP2M1 to lipid droplets and that the observed defect in HCV assembly following disruption of core-AP2M1 binding correlates with accumulation of core on lipid droplets, reduced core colocalization with E2 and reduced core localization to trans-Golgi network (TGN), the presumed site of viral particles maturation. Furthermore, AAK1 and GAK, serine/threonine kinases known to stimulate binding of AP2M1 to host cargo proteins, regulate core-AP2M1 binding and are essential for HCV assembly. Last, approved anti-cancer drugs that inhibit AAK1 or GAK not only disrupt core-AP2M1 binding, but also significantly inhibit HCV assembly and infectious virus production. These results validate viral-host interactions essential for HCV assembly and yield compounds for pharmaceutical development. Novel antiviral strategies are needed to combat the HCV pandemic. Understanding viral-host determinants involved in mediating assembly is critical for the development of drugs targeting this stage of the HCV life cycle. We identified a conserved heretofore unrecognized tyrosine motif within core, which is homologous to sorting signals within host cargo proteins that are recognized by AP2M1, a membrane trafficking protein. By combining novel proteomic techniques with molecular virology, RNAi, dominant-interfering, and pharmacological approaches, we show that this motif mediates core binding to AP2M1 and HCV assembly and that AP2M1 is essential for HCV assembly. Core's tryosine motif recruits AP2M1 to lipid droplets, the site of viral assembly, and disruption of core-AP2M1 binding alters core's sub-cellular localization and colocalization with the envelope protein E2. AAK1 and GAK, host kinases that stimulate AP2M1's interactions with cargo proteins, regulate core-AP2M1 binding and are essential for HCV assembly. Last, we discovered kinase inhibitors, which bind AAK1 or GAK and disrupt core-AP2M1 binding and HCV assembly. Our study provides insight into mechanisms of HCV assembly and yields candidate targets and compounds for pharmaceutical development. Since some of the discovered compounds are approved anti-cancer drugs, there may be an opportunity for repurposing them as antivirals.
Collapse
Affiliation(s)
- Gregory Neveu
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Rina Barouch-Bentov
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Amotz Ziv-Av
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Doron Gerber
- The Mina and Everard Goodman Faculty of Life Sciences and The Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Yves Jacob
- Department of Virology, Unité de Génétique, Papillomavirus et Cancer Humain (GPCH), Pasteur Institute, Paris, France
| | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| |
Collapse
|
27
|
Gan J, Zhu J, Yan G, Liu Y, Yang P, Liu B. Periodic mesoporous organosilica as a multifunctional nanodevice for large-scale characterization of membrane proteins. Anal Chem 2012; 84:5809-15. [PMID: 22663254 DOI: 10.1021/ac301146a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A versatile protocol has been developed for large-scale characterization of hydrophobic membrane proteins based on the periodic mesoporous organosilica (PMO) acting as both an extractor for hydrophobic substrate capture and a nanoreactor for efficient in situ digestion. With introduction of organic groups in the pore frameworks and the presence of hydrophilic silanol groups on the surface, PMO can be well-dispersed into not only an organic solution to concentrate the dissolved membrane proteins but also an aqueous solution containing enzymes for sequential rapid proteolysis in the nanopores. The unique amphiphilic property of PMO ensures a facile switch in different solutions to realize the processes of substrate dissolution, enrichment, and digestion effectively. Furthermore, this novel PMO-assisted protocol has been successfully applied for identification of complex membrane proteins extracted from mouse liver as proof of general applicability.
Collapse
Affiliation(s)
- Jinrui Gan
- Department of Chemistry, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | | | | | | | | | | |
Collapse
|
28
|
Altelaar AFM, Heck AJR. Trends in ultrasensitive proteomics. Curr Opin Chem Biol 2012; 16:206-13. [DOI: 10.1016/j.cbpa.2011.12.011] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 12/19/2011] [Accepted: 12/19/2011] [Indexed: 11/27/2022]
|
29
|
Abstract
Proteomic analysis requires the combination of an extensive suite of technologies including protein processing and separation, micro-flow HPLC, MS and bioinformatics. Although proteomic technologies are still in flux, approaches that bypass gel electrophoresis (gel-free approaches) are dominating the field of proteomics. Along with the development of gel-free proteomics, came the development of devices for the processing of proteomic samples termed proteomic reactors. These microfluidic devices provide rapid, robust and efficient pre-MS sample procession by performing protein sample preparation/concentration, digestion and peptide fractionation. The proteomic reactor has advanced in two major directions: immobilized enzyme reactor and ion exchange-based proteomic reactor. This review summarizes the technical developments and biological applications of the proteomic reactor over the last decade.
Collapse
Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, ON, Canada
| | | | | | | | | |
Collapse
|