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Cruz Otero JD, Jager M, Armien AG, Miller A, Stokol T. Granular variant of a histiocytic tumor on the toe of a cat: Case report and literature review. Vet Clin Pathol 2023; 52:102-107. [PMID: 35751153 DOI: 10.1111/vcp.13152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/13/2022] [Accepted: 04/25/2022] [Indexed: 11/28/2022]
Abstract
A 16-year-old female spayed domestic shorthaired cat was examined for lameness and a mass on the fourth digit of the right hindlimb. Cytologic examination of an aspirate of the mass revealed large discrete cells admixed with low numbers of well-granulated mast cells. The discrete cells contained single to many variably sized light pink to purple granules in their cytoplasm and had pleomorphic nuclei, with intranuclear cytoplasmic inclusions. Karyomegalic, binucleated and multinucleated cells were seen. Histologic examination of formalin-fixed sections of the excised mass showed a mildly infiltrative, unencapsulated, multinodular dermal mass that extended into the subcutis and consisted of similar discrete cells. On immunohistochemical staining, the tumor cells expressed ionized calcium-binding adapter molecule 1 (Iba1) and CD18. The tumor cells did not express CD3, CD20, CD117, pancytokeratin (AE1/AE3), melanoma antigen (Melan-A), multiple myeloma oncogene-1 (MUM1), melanoma-associated antigen (PNL-2), and S-100. Low numbers of tumor cells expressed CD204 and protein gene product 9.5 (PGP9.5). Granules were variably positive for Periodic-acid Schiff (PAS) and Alcian blue. On transmission electron microscopy, the cells contained filopodia, abundant endoplasmic reticulum, and moderate numbers of low-density membrane-bound granules. This case documents a previously undescribed granular variant of a histiocytic tumor in a cat.
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Affiliation(s)
- José D Cruz Otero
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Mason Jager
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Anibal G Armien
- California Animal Health and Food Safety Laboratory System (CAHFS), School of Veterinary Medicine, University of California, Davis, California, USA
| | - Andrew Miller
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Tracy Stokol
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Xiao Q, Zhang F, Xu L, Yue L, Kon OL, Zhu Y, Guo T. High-throughput proteomics and AI for cancer biomarker discovery. Adv Drug Deliv Rev 2021; 176:113844. [PMID: 34182017 DOI: 10.1016/j.addr.2021.113844] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023]
Abstract
Biomarkers are assayed to assess biological and pathological status. Recent advances in high-throughput proteomic technology provide opportunities for developing next generation biomarkers for clinical practice aided by artificial intelligence (AI) based techniques. We summarize the advances and limitations of cancer biomarkers based on genomic and transcriptomic analysis, as well as classical antibody-based methodologies. Then we review recent progresses in mass spectrometry (MS)-based proteomics in terms of sample preparation, peptide fractionation by liquid chromatography (LC) and mass spectrometric data acquisition. We highlight applications of AI techniques in high-throughput clinical studies as compared with clinical decisions based on singular features. This review sets out our approach for discovering clinical biomarkers in studies using proteomic big data technology conjoined with computational and statistical methods.
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Zhang Y, Xu C, Ye Q, Tong L, Jiang H, Zhu X, Huang L, Lin W, Fu H, Wang J, Persson PB, Lai EY, Mao J. Podocyte apoptosis in diabetic nephropathy by BASP1 activation of the p53 pathway via WT1. Acta Physiol (Oxf) 2021; 232:e13634. [PMID: 33615732 DOI: 10.1111/apha.13634] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/05/2021] [Accepted: 02/18/2021] [Indexed: 12/20/2022]
Abstract
AIMS Diabetic nephropathy (DN) is a leading cause of end-stage renal disease. BASP1 (brain acid-soluble protein) is up-regulated in podocyte-specific protein phosphatase 2A knockout mice (Pod-PP2A-KO) that develop kidney dysfunction. Here, we explore the role of BASP1 for podocytes in DN. METHODS BASP1 was assessed in kidneys from DN patients and DN mouse models, podocyte specific BASP1 knockout mice (Pod-BASP1-KO mice) were generated and studied in vivo. Furthermore, podocyte injury and apoptosis were measured after BASP1 knockdown and overexpression in a mouse podocyte cell line (MPC5). Potential signalling pathways involved in podocyte apoptosis were detected. RESULTS BASP1 expression was up-regulated in DN patients compared to normal controls. BASP1 specific deletion in podocytes protected against podocyte injury by reducing the loss of expression of slit diaphragm molecules and foot process effacement in the DN model. BASP1 promoted actin cytoskeleton rearrangements and apoptosis in the MPC5 podocyte line. Molecules involved in the p53 pathway were down-regulated in BASP1 knockdown podocytes treated with high glucose compared to controls. BASP1 promoted podocyte apoptosis and P53 pathway activation through co-repression with Wilms' tumour 1 transcription factor (WT1). CONCLUSION BASP1 activates the p53 pathway through modulation of WT1 to induce podocyte apoptosis in diabetic nephropathy.
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Affiliation(s)
- Yingying Zhang
- Department of Nephrology The Children Hospital of Zhejiang University School of MedicineNational Clinical Research Center for Child HealthNational Children’s Regional Medical Center Hangzhou China
| | - Chengxian Xu
- Department of Nephrology The Children Hospital of Zhejiang University School of MedicineNational Clinical Research Center for Child HealthNational Children’s Regional Medical Center Hangzhou China
| | - Qing Ye
- Department of Nephrology The Children Hospital of Zhejiang University School of MedicineNational Clinical Research Center for Child HealthNational Children’s Regional Medical Center Hangzhou China
| | - Lingxiao Tong
- Department of Nephrology The Children Hospital of Zhejiang University School of MedicineNational Clinical Research Center for Child HealthNational Children’s Regional Medical Center Hangzhou China
| | - Hong Jiang
- Kidney Disease Center The First Affiliated HospitalZhejiang University School of Medicine Hangzhou China
| | - Xiujuan Zhu
- Department of Nephrology The Children Hospital of Zhejiang University School of MedicineNational Clinical Research Center for Child HealthNational Children’s Regional Medical Center Hangzhou China
| | - Limin Huang
- Department of Nephrology The Children Hospital of Zhejiang University School of MedicineNational Clinical Research Center for Child HealthNational Children’s Regional Medical Center Hangzhou China
| | - Weiqiang Lin
- Institute of Translational Medicine Zhejiang University School of Medicine Hangzhou China
| | - Haidong Fu
- Department of Nephrology The Children Hospital of Zhejiang University School of MedicineNational Clinical Research Center for Child HealthNational Children’s Regional Medical Center Hangzhou China
| | - Jingjing Wang
- Department of Nephrology The Children Hospital of Zhejiang University School of MedicineNational Clinical Research Center for Child HealthNational Children’s Regional Medical Center Hangzhou China
| | - Pontus B. Persson
- Institute of Vegetative Physiology Charité–Universitätsmedizin Berlincorporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of Health Berlin Germany
| | - En Yin Lai
- Kidney Disease Center The First Affiliated HospitalZhejiang University School of Medicine Hangzhou China
- Institute of Vegetative Physiology Charité–Universitätsmedizin Berlincorporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of Health Berlin Germany
- Department of Physiology Zhejiang University School of Medicine Hangzhou China
| | - Jianhua Mao
- Department of Nephrology The Children Hospital of Zhejiang University School of MedicineNational Clinical Research Center for Child HealthNational Children’s Regional Medical Center Hangzhou China
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Liu J, Zhang H, Yan L, Kerr PG, Zhang S, Wu Y. Electron transport, light energy conversion and proteomic responses of periphyton in photosynthesis under exposure to AgNPs. J Hazard Mater 2021; 401:123809. [PMID: 33113741 DOI: 10.1016/j.jhazmat.2020.123809] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/10/2020] [Accepted: 08/21/2020] [Indexed: 05/09/2023]
Abstract
Silver nanoparticles (AgNPs) including a mix of intact nanoparticle-Ag and 'free' Ag+ pose high risks to benthic photoautotrophs, but the photosynthetic responses of benthic microbial aggregates to AgNPs still remain largely unknown. Here, periphyton and Nostoc were used to elucidate the photosynthetic responses of benthic algae community to intact nanoparticle-Ag and Ag+. During exposure, both intact nanoparticle-Ag and Ag+ imposed negative effects on photosynthesis of benthic algae, but via different pathways. Specifically, Ag+ had stronger effects on damaging the oxygen-evolving complex (OEC) and thylakoid membrane than intact nanoparticle-Ag. Ag+ also suppressed electron transfer from QA to QB, and impaired phycobilisome. Intact nanoparticle-Ag inhibited the expression of PsbD and PsbL in PSII, but prompted the ROS scavenging capacity. In response to the stress of AgNPs, the benthic algae increased light energy absorption to maintain the electron transport efficiency, and up-regulated PSI reaction center protein (PsaA) to compensate the degraded PSII. These results reveal how intact nanoparticle-Ag and Ag+ influence electron transport, energy conversion and protein expression in the photosynthesis of periphyton, and provide deep insights into the responses of benthic photoautotrophs to different components of AgNPs.
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Affiliation(s)
- Junzhuo Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang, 443605, China.
| | - Huijie Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008, China; College of Agricultural Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liying Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008, China; Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, China
| | - Philip G Kerr
- School of Biomedical Sciences, Charles Sturt University, Boorooma St., Wagga Wagga, NSW, 2678, Australia
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang, 443605, China.
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Li K, Xian M, Chen C, Liang S, Chen L, Wang S. Proteomic Assessment of iTRAQ-Based NaoMaiTong in the Treatment of Ischemic Stroke in Rats. Evid Based Complement Alternat Med 2019; 2019:5107198. [PMID: 31223330 DOI: 10.1155/2019/5107198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/17/2019] [Indexed: 01/17/2023]
Abstract
Background NaoMaiTong (NMT) is widely used in the treatment of cerebral ischemia but the molecular details of its beneficial effects remain poorly characterized. Materials and Methods In this study, we used iTRAQ using 2D LC-MS/MS technology to investigate the cellular mechanisms governing the protective effects of NMT. The transient middle cerebral artery occlusion (MCAO) rat model was established and evaluated. The degree of cerebral ischemia was assessed through scoring for nerve injury symptoms and through the assessment of the areas of cerebral infarction. Brain tissues were subjected to analysis by iTRAQ. High-pH HPLC and RSLC-MS/MS analysis were performed to detect differentially expressed proteins (DEPs) between the treatment groups (Sham, MCAO, and NMT). Bioinformatics were employed for data analysis and DEPs were validated by western blot. Results The results showed that NMT offers protection to the neurological damage caused by MCAO and was found to reduce the areas of cerebral infarction. We detected 3216 DEPs via mass spectrometry. Of these proteins, 21 displayed altered expression following NMT intervention. These included DEPs involved in translation, cell cycle regulation, cellular nitrogen metabolism, and stress responses. Pathway analysis revealed seven key DEPs that were enriched in ribosomal synthesis pathways, tight junction formation, and regulation of the actin cytoskeleton. According to protein-protein interaction analysis, RPL17, Tuba, and Rac1 were affected by NMT treatment, which was validated by western blot analysis. Discussion We therefore identify new pharmacodynamic mechanisms of NMT for the prevention and treatment of ischemic stroke. These DEPs reveal new targets to prevent ischemic stroke induced neuronal damage.
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Shereck E, Day NS, Awasthi A, Ayello J, Chu Y, McGuinn C, van de Ven C, Lim MS, Cairo MS. Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56 Dim NK cells. Innate Immun 2019; 25:294-304. [PMID: 31068047 PMCID: PMC6830905 DOI: 10.1177/1753425919846584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Unrelated cord blood (CB) is an excellent alternative as an allogeneic donor
source for stem cell transplantation. CB transplantation is associated with
lower incidence of severe acute graft versus host disease (GVHD) and chronic
GVHD but similar rates of malignant relapse compared with other unrelated donor
cell transplants. NK cells are critical innate immune components and the
comparison of CB vs. peripheral blood (PB) NK cells is relatively unknown. NK
cell receptor expression, cell function, and maturation may play a role in the
risk of relapse after CB transplant. We investigated CB vs. PB NK cell subset
cytotoxicity, function, receptor expression, and genomic and proteomic
signatures. The CB CD56dim compared with PB CD56dim
demonstrated significantly increased expression of NKG2A and NKG2D,
respectively. CB vs. PB CD56dim NK cells had significantly decreased
in vitro cytotoxicity against a variety of non-Hodgkin
lymphoma targets. Various proteins were significantly under- and over-expressed
in CB vs. PB CD56dim NK cells. Microarray analyses and qRT-PCR in CB
vs. PB CD56dim demonstrated significantly increased expression of
genes in cell regulation and development of apoptosis, respectively. In summary,
CB vs. PB CD56dim NK cells appear to be earlier in development, have
decreased functional activity, and increased capacity for programmed cell death,
suggesting that CB NK cells require functional and maturational stimulation to
achieve similar functional levels as PB CD56dim NK cells.
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Affiliation(s)
- Evan Shereck
- 1 Department of Pediatrics, Oregon Health and Science University, Portland, 97239, USA
| | - Nancy S Day
- 2 Department of Pediatrics, Columbia University, New York, USA
| | - Aradhana Awasthi
- 3 Department of Pediatrics, New York Medical College, Valhalla, USA
| | - Janet Ayello
- 3 Department of Pediatrics, New York Medical College, Valhalla, USA
| | - Yaya Chu
- 3 Department of Pediatrics, New York Medical College, Valhalla, USA
| | | | | | - Megan S Lim
- 4 Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA
| | - Mitchell S Cairo
- 3 Department of Pediatrics, New York Medical College, Valhalla, USA.,5 Department of Medicine, New York Medical College, Valhalla, USA.,6 Department of Pathology, New York Medical College, Valhalla, USA.,7 Department of Microbiology and Immunology, New York Medical College, Valhalla, USA.,8 Department Cell Biology and Anatomy, New York Medical College, Valhalla, USA
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Zhang J, Liang R, Wei J, Ye J, He Q, ChunlingYuan, Ye J, Li Y, Liu Z, Lin Y. Identification of Candidate Biomarkers in Malignant Ascites from Patients with Hepatocellular Carcinoma by iTRAQ-Based Quantitative Proteomic Analysis. Biomed Res Int 2018; 2018:5484976. [PMID: 30345303 DOI: 10.1155/2018/5484976] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/05/2018] [Accepted: 09/02/2018] [Indexed: 12/13/2022]
Abstract
Almost all the patients with hepatocellular carcinoma (HCC) at advanced stage experience pathological changes of chronic liver cirrhosis, which generally leads to moderate ascites. Recognition of novel biomarkers in malignant ascites could be favorable for establishing a diagnosis for the HCC patients with ascites, and even predicting prognosis, such as risk of distant metastasis. To distinguish the proteomic profiles of malignant ascites in HCC patients from those with nonmalignant liver cirrhosis, an iTRAQ pipeline was built up to analyze the differentially distributed proteins in the malignant ascites from HCC patients (n=10) and benign ascites from hepatic decompensation (HD) controls (n=9). In total, 112 differentially distributed proteins were identified, of which 69 proteins were upregulated and 43 proteins were downregulated (ratio <0.667 or >1.3, respectively) in the malignant ascites. Moreover, 19 upregulated proteins (including keratin 1 protein and rheumatoid factor RF-IP20, ratio>1.5) and 8 downregulated proteins (including carbonic anhydrase 1, ratio<0.667) were identified from malignant ascites samples. Functional categories analyses indicated that membrane proteins, ion regulation, and amino acid metabolism are implicated in the formation of HCC malignant ascites. Pathways mapping revealed that glycolysis/gluconeogenesis and complement/coagulation cascades are the mostly affected cell life activities in HCC malignant ascites, suggesting the key factors in these pathways such as Enolase-1 and fibrinogen are potential ascitic fluid based biomarkers for diagnosis and prognosis for HCC.
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Ha KD, Bidlingmaier SM, Su Y, Lee NK, Liu B. Identification of Novel Macropinocytosing Human Antibodies by Phage Display and High-Content Analysis. Methods Enzymol 2017; 585:91-110. [PMID: 28109445 PMCID: PMC8671048 DOI: 10.1016/bs.mie.2016.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Internalizing antibodies have great potential for the development of targeted therapeutics. Antibodies that internalize via the macropinocytosis pathway are particularly promising since macropinocytosis is capable of mediating rapid, bulk uptake and is selectively upregulated in many cancers. We hereby describe a method for identifying antibodies that internalize via macropinocytosis by screening phage-displayed single-chain antibody selection outputs with an automated fluorescent microscopy-based high-content analysis platform. Furthermore, this method can be similarly applied to other endocytic pathways if other fluorescent, pathway-specific, soluble markers are available.
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Affiliation(s)
| | | | | | | | - Bin Liu
- Corresponding author Department of Anesthesia, University of California at San Francisco, 1001 Potrero Ave., Box 1305, San Francisco, CA 94110-1305,
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Plesofsky N, Higgins L, Markowski T, Brambl R. Glucose Starvation Alters Heat Shock Response, Leading to Death of Wild Type Cells and Survival of MAP Kinase Signaling Mutant. PLoS One 2016; 11:e0165980. [PMID: 27870869 DOI: 10.1371/journal.pone.0165980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022] Open
Abstract
A moderate heat shock induces Neurospora crassa to synthesize large quantities of heat shock proteins that are protective against higher, otherwise lethal temperatures. However, wild type cells do not survive when carbohydrate deprivation is added to heat shock. In contrast, a mutant strain defective in a stress-activated protein kinase does survive the combined stresses. In order to understand the basis for this difference in survival, we have determined the relative levels of detected proteins in the mutant and wild type strain during dual stress, and we have identified gene transcripts in both strains whose quantities change in response to heat shock or dual stress. These data and supportive experimental evidence point to reasons for survival of the mutant strain. By using alternative respiratory mechanisms, these cells experience less of the oxidative stress that proves damaging to wild type cells. Of central importance, mutant cells recycle limited resources during dual stress by undergoing autophagy, a process that we find utilized by both wild type and mutant cells during heat shock. Evidence points to inappropriate activation of TORC1, the central metabolic regulator, in wild type cells during dual stress, based upon behavior of an additional signaling mutant and inhibitor studies.
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Aslam B, Basit M, Nisar MA, Khurshid M, Rasool MH. Proteomics: Technologies and Their Applications. J Chromatogr Sci 2016; 55:182-196. [PMID: 28087761 DOI: 10.1093/chromsci/bmw167] [Citation(s) in RCA: 429] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 07/25/2016] [Accepted: 09/08/2016] [Indexed: 12/12/2022]
Abstract
Proteomics involves the applications of technologies for the identification and quantification of overall proteins present content of a cell, tissue or an organism. It supplements the other "omics" technologies such as genomic and transcriptomics to expound the identity of proteins of an organism, and to cognize the structure and functions of a particular protein. Proteomics-based technologies are utilized in various capacities for different research settings such as detection of various diagnostic markers, candidates for vaccine production, understanding pathogenicity mechanisms, alteration of expression patterns in response to different signals and interpretation of functional protein pathways in different diseases. Proteomics is practically intricate because it includes the analysis and categorization of overall protein signatures of a genome. Mass spectrometry with LC-MS-MS and MALDI-TOF/TOF being widely used equipment is the central among current proteomics. However, utilization of proteomics facilities including the software for equipment, databases and the requirement of skilled personnel substantially increase the costs, therefore limit their wider use especially in the developing world. Furthermore, the proteome is highly dynamic because of complex regulatory systems that control the expression levels of proteins. This review efforts to describe the various proteomics approaches, the recent developments and their application in research and analysis.
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Affiliation(s)
- Bilal Aslam
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Madiha Basit
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Muhammad Atif Nisar
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University, Faisalabad, Pakistan .,College of Allied Health Professionals, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
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Maes E, Hadiwikarta WW, Mertens I, Baggerman G, Hooyberghs J, Valkenborg D. CONSTANd : A Normalization Method for Isobaric Labeled Spectra by Constrained Optimization. Mol Cell Proteomics 2016; 15:2779-90. [PMID: 27302888 DOI: 10.1074/mcp.m115.056911] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Indexed: 01/05/2023] Open
Abstract
In quantitative proteomics applications, the use of isobaric labels is a very popular concept as they allow for multiplexing, such that peptides from multiple biological samples are quantified simultaneously in one mass spectrometry experiment. Although this multiplexing allows that peptide intensities are affected by the same amount of instrument variability, systematic effects during sample preparation can also introduce a bias in the quantitation measurements. Therefore, normalization methods are required to remove this systematic error. At present, a few dedicated normalization methods for isobaric labeled data are at hand. Most of these normalization methods include a framework for statistical data analysis and rely on ANOVA or linear mixed models. However, for swift quality control of the samples or data visualization a simple normalization technique is sufficient. To this aim, we present a new and easy-to-use data-driven normalization method, named CONSTANd. The CONSTANd method employs constrained optimization and prior information about the labeling strategy to normalize the peptide intensities. Further, it allows maintaining the connection to any biological effect while reducing the systematic and technical errors. As a result, peptides can not only be compared directly within a multiplexed experiment, but are also comparable between other isobaric labeled datasets from multiple experimental designs that are normalized by the CONSTANd method, without the need to include a reference sample in every experimental setup. The latter property is especially useful when more than six, eight or ten (TMT/iTRAQ) biological samples are required to detect differential peptides with sufficient statistical power and to optimally make use of the multiplexing capacity of isobaric labels.
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Affiliation(s)
- Evelyne Maes
- From the: ‡Applied Bio & molecular Systems, VITO, Boeretang 200, 2400 Mol, Belgium; §Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | | | - Inge Mertens
- From the: ‡Applied Bio & molecular Systems, VITO, Boeretang 200, 2400 Mol, Belgium; §Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Geert Baggerman
- From the: ‡Applied Bio & molecular Systems, VITO, Boeretang 200, 2400 Mol, Belgium; §Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Jef Hooyberghs
- From the: ‡Applied Bio & molecular Systems, VITO, Boeretang 200, 2400 Mol, Belgium; ¶Theoretical Physics, Hasselt University, Agoralaan 1, 3590 Diepenbeek, Belgium
| | - Dirk Valkenborg
- From the: ‡Applied Bio & molecular Systems, VITO, Boeretang 200, 2400 Mol, Belgium; §Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; ‖Center for Statistics, Hasselt University, Agoralaan 1, 3590 Diepenbeek, Belgium
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Reck J, Schauer AM, VanderWaal Mills K, Bower R, Tritschler D, Perrone CA, Porter ME. The role of the dynein light intermediate chain in retrograde IFT and flagellar function in Chlamydomonas. Mol Biol Cell 2016; 27:2404-22. [PMID: 27251063 PMCID: PMC4966982 DOI: 10.1091/mbc.e16-03-0191] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/26/2016] [Indexed: 12/28/2022] Open
Abstract
The assembly of cilia and flagella depends on the activity of two microtubule motor complexes, kinesin-2 and dynein-2/1b, but the specific functions of the different subunits are poorly defined. Here we analyze Chlamydomonas strains expressing different amounts of the dynein 1b light intermediate chain (D1bLIC). Disruption of D1bLIC alters the stability of the dynein 1b complex and reduces both the frequency and velocity of retrograde intraflagellar transport (IFT), but it does not eliminate retrograde IFT. Flagellar assembly, motility, gliding, and mating are altered in a dose-dependent manner. iTRAQ-based proteomics identifies a small subset of proteins that are significantly reduced or elevated in d1blic flagella. Transformation with D1bLIC-GFP rescues the mutant phenotypes, and D1bLIC-GFP assembles into the dynein 1b complex at wild-type levels. D1bLIC-GFP is transported with anterograde IFT particles to the flagellar tip, dissociates into smaller particles, and begins processive retrograde IFT in <2 s. These studies demonstrate the role of D1bLIC in facilitating the recycling of IFT subunits and other proteins, identify new components potentially involved in the regulation of IFT, flagellar assembly, and flagellar signaling, and provide insight into the role of D1bLIC and retrograde IFT in other organisms.
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Affiliation(s)
- Jaimee Reck
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 R&D Systems, Minneapolis, MN 55413
| | - Alexandria M Schauer
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108
| | - Kristyn VanderWaal Mills
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 Anoka Technical College, Anoka, MN 55303
| | - Raqual Bower
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
| | - Douglas Tritschler
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
| | - Catherine A Perrone
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 Medtronic, Minneapolis, MN 55432
| | - Mary E Porter
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
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Butterick TA, Hocum Stone L, Duffy C, Holley C, Cabrera JA, Crampton M, Ward HB, Kelly RF, McFalls EO. Pioglitazone increases PGC1-α signaling within chronically ischemic myocardium. Basic Res Cardiol 2016; 111:37. [PMID: 27138931 DOI: 10.1007/s00395-016-0555-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/07/2016] [Indexed: 11/29/2022]
Abstract
The peroxisome proliferator-activated receptor (PPAR)-γ drug pioglitazone (PIO) has been shown to protect tissue against oxidant stress. In a swine model of chronic myocardial ischemia, we tested whether PIO increases PGC1-α signaling and the expression of mitochondrial antioxidant peptides. Eighteen pigs underwent a thoracotomy with placement of a fixed constrictor around the LAD artery. At 8 weeks, diet was supplemented with either PIO (3 mg/kg) or placebo for 4 weeks. Regional myocardial function and blood flow were determined at the time of the terminal study. PGC1-α expression was quantified from nuclear membranes by gels and respiration, oxidant stress markers and proteomics by iTRAQ were determined from isolated mitochondria. In the chronically ischemic LAD region, wall thickening from the PIO and control groups was 42 ± 6 and 45 ± 5 %, respectively (NS) with no intergroup differences in basal blood flow (0.72 ± 0.04 versus 0.74 ± 0.04 ml/min g, respectively; NS). In the PIO group, the expression of nuclear bound PGC1-α was higher (11.3 ± 2.6 versus 4.4 ± 1.4 AU; P < 0.05) and the content of mitochondrial antioxidant peptides including superoxide dismutase 2, aldose reductase, glutathione S-transferase and thioredoxin reductase were greater than controls. Although isolated mitochondria from the PIO group showed lower state 3 respiration (102 ± 13 versus 161 ± 22 nmol/min mg; P < 0.05), no differences in oxidant stress were noted by protein carbonyl (1.7 ± 0.7 versus 1.1 ± 0.1 nmol/mg). Chronic pioglitazone does not reduce regional myocardial blood flow or function in a swine model of chronic myocardial ischemia, but may have an important role in increasing expression of antioxidant proteins through PGC1-α signaling.
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Affiliation(s)
- Tammy A Butterick
- Cardiology and Cardiothoracic Surgery Sections, Cardiology (111C), VA Medical Center, 1 Veterans Drive, Minneapolis, MN, 55417, USA.,Department of Surgery, University of Minnesota, Minneapolis, USA.,Cardiology and Cardiothoracic Surgery Sections, Department of Nutrition, VA Medical Center, Minneapolis, USA.,Minnesota Obesity Center, University of Minnesota, 1334 Eckles Avenue, St. Paul, MN, 55108, USA
| | - Laura Hocum Stone
- Cardiology and Cardiothoracic Surgery Sections, Cardiology (111C), VA Medical Center, 1 Veterans Drive, Minneapolis, MN, 55417, USA.,Department of Surgery, University of Minnesota, Minneapolis, USA
| | - Cayla Duffy
- Cardiology and Cardiothoracic Surgery Sections, Cardiology (111C), VA Medical Center, 1 Veterans Drive, Minneapolis, MN, 55417, USA.,Department of Surgery, University of Minnesota, Minneapolis, USA.,Cardiology and Cardiothoracic Surgery Sections, Department of Nutrition, VA Medical Center, Minneapolis, USA
| | - Christopher Holley
- Cardiology and Cardiothoracic Surgery Sections, Cardiology (111C), VA Medical Center, 1 Veterans Drive, Minneapolis, MN, 55417, USA.,Department of Surgery, University of Minnesota, Minneapolis, USA
| | - Jesús A Cabrera
- Cardiology and Cardiothoracic Surgery Sections, Cardiology (111C), VA Medical Center, 1 Veterans Drive, Minneapolis, MN, 55417, USA.,Department of Surgery, University of Minnesota, Minneapolis, USA
| | - Melanie Crampton
- Cardiology and Cardiothoracic Surgery Sections, Cardiology (111C), VA Medical Center, 1 Veterans Drive, Minneapolis, MN, 55417, USA.,Department of Surgery, University of Minnesota, Minneapolis, USA
| | - Herbert B Ward
- Cardiology and Cardiothoracic Surgery Sections, Cardiology (111C), VA Medical Center, 1 Veterans Drive, Minneapolis, MN, 55417, USA.,Department of Surgery, University of Minnesota, Minneapolis, USA
| | - Rosemary F Kelly
- Cardiology and Cardiothoracic Surgery Sections, Cardiology (111C), VA Medical Center, 1 Veterans Drive, Minneapolis, MN, 55417, USA.,Department of Surgery, University of Minnesota, Minneapolis, USA
| | - Edward O McFalls
- Cardiology and Cardiothoracic Surgery Sections, Cardiology (111C), VA Medical Center, 1 Veterans Drive, Minneapolis, MN, 55417, USA. .,Department of Surgery, University of Minnesota, Minneapolis, USA.
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14
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Hwang HI, Lee TH, Kang KJ, Ryu CJ, Jang YJ. Immunomic Screening of Cell Surface Molecules on Undifferentiated Human Dental Pulp Stem Cells. Stem Cells Dev 2015; 24:1934-45. [PMID: 25919113 DOI: 10.1089/scd.2014.0493] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Human adult dental pulp tissue is a source of adult stem cells that have a potential to differentiate into various tissues, although the primary cell suspensions cultured from pulp tissue are mixtures of both stem cell and nonstem cell populations with heterogeneous phenotypes and various differentiation efficiencies. Therefore, cell surface protein markers on dental pulp stem cells are critical for detection and purification of stem cell populations. Yet, little is known about the cell surface molecules that are specifically associated with the undifferentiated and progenitor state of human adult dental pulp stem cells (hDPSCs). Presently, cell surface proteins expressed on hDPSCs were assessed by screening surface molecules specifically expressed on dentinogenic progenitors. Using a decoy immunization strategy, a set of monoclonal antibodies (MAbs) was generated against undifferentiated pulp progenitor cells. Forty-five hybridomas produced MAbs that interacted weakly, if at all, to differentiated pulp cells. Of these, 19 MAbs (18 IgG, 1 IgM) recognized surface molecules on undifferentiated hDPSCs. By multicolor flow cytometric analysis, 40%-60% of newly identified MAb-positive cells were demonstrated to be positive for the CD44 and CD90 mesenchymal markers. When MAb-positive cells were sorted from the heterogeneous pulp cell suspension, mineralization efficiency was increased three to five times compared with MAb-negative cells. The results suggest that the decoy immunization is an efficient method for isolation of MAbs against dentinogenic progenitors. These MAbs will be helpful for identification and enrichment of hDPSCs for efficient dentin regeneration.
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Affiliation(s)
- Hyo-In Hwang
- 1 Department of Nanobiomedical Science, BK21 PLUS Global Research Center for Regenerative Medicine, Dankook University , Cheonan, Korea
| | - Tae-Hyung Lee
- 1 Department of Nanobiomedical Science, BK21 PLUS Global Research Center for Regenerative Medicine, Dankook University , Cheonan, Korea
| | - Kyung-Jung Kang
- 1 Department of Nanobiomedical Science, BK21 PLUS Global Research Center for Regenerative Medicine, Dankook University , Cheonan, Korea
| | - Chun-Jeih Ryu
- 2 Department of Bioscience and Biotechnology, Sejong University , Seoul, Korea
| | - Young-Joo Jang
- 1 Department of Nanobiomedical Science, BK21 PLUS Global Research Center for Regenerative Medicine, Dankook University , Cheonan, Korea.,3 Laboratory of Oral Biochemistry, the School of Dentistry, Dankook University , Cheonan, Korea
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15
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Abstract
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Mass spectrometry plays a key role
in relative quantitative comparisons
of proteins in order to understand their functional role in biological
systems upon perturbation. In this review, we review studies that
examine different aspects of isobaric labeling-based relative quantification
for shotgun proteomic analysis. In particular, we focus on different
types of isobaric reagents and their reaction chemistry (e.g., amine-,
carbonyl-, and sulfhydryl-reactive). Various factors, such as ratio
compression, reporter ion dynamic range, and others, cause an underestimation
of changes in relative abundance of proteins across samples, undermining
the ability of the isobaric labeling approach to be truly quantitative.
These factors that affect quantification and the suggested combinations
of experimental design and optimal data acquisition methods to increase
the precision and accuracy of the measurements will be discussed.
Finally, the extended application of isobaric labeling-based approach
in hyperplexing strategy, targeted quantification, and phosphopeptide
analysis are also examined.
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Affiliation(s)
- Navin Rauniyar
- Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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16
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Robbins ML, Roy A, Wang PH, Gaffoor I, Sekhon RS, de O Buanafina MM, Rohila JS, Chopra S. Comparative proteomics analysis by DIGE and iTRAQ provides insight into the regulation of phenylpropanoids in maize. J Proteomics 2013; 93:254-75. [PMID: 23811284 DOI: 10.1016/j.jprot.2013.06.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 06/06/2013] [Accepted: 06/10/2013] [Indexed: 12/17/2022]
Abstract
UNLABELLED The maize pericarp color1 (p1) gene encodes a Myb transcription factor that regulates the accumulation of 3-deoxyflavonoid pigments called phlobaphenes. The Unstable factor for orange1 (Ufo1) is a dominant epigenetic modifier of the p1 that results in ectopic pigmentation in pericarp. Presence of Ufo1-1 correlates with pleiotropic growth and developmental defects. To investigate the Ufo1-1-induced changes in the proteome, we conducted comparative proteomics analysis of P1-wr; Ufo1-1 pericarps using the 2-D DIGE and iTRAQ techniques. Most of the identified proteins were found to be involved in glycolysis, protein synthesis and modification, flavonoid and lignin biosynthesis and defense responses. Further, immunoblot analysis of internode protein extracts demonstrated that caffeoyl CoA O-methyltransferase (COMT) is post-transcriptionally down regulated in P1-wr; Ufo1-1 plants. Consistent with the down regulation of COMT, the concentrations of p-coumaric acid, syringaldehydes, and lignin are reduced in P1-wr; Ufo1-1 internodes. The reductions in these phenylpropanoids correlate with the bent stalk and stunted growth of P1-wr; Ufo1-1 plants. Finally, over-expression of the p1 in transgenic plants is also correlated with a lodging phenotype and reduced COMT expression. We conclude that ectopic expression of p1 can result in developmental defects that are correlated with altered regulation and synthesis of phenylpropanoid compounds including lignin. BIOLOGICAL SIGNIFICANCE Transcription factors have specific expression patterns that ensure that the biochemical pathways under their control are active in relevant tissues. Plant breeders can select for alleles of transcription factors that produce desirable expression patterns to improve a plant's growth, development, and defense against insects and pathogens. The resulting de novo accumulation of metabolites in plant tissues in significant quantities could have beneficial and/or detrimental consequences. To understand this problem we investigated how the aberrant expression of a classically-studied transcription factor pericarp color1 (p1) which regulates phenylpropanoid metabolism, affects the maize proteome in pericarp tissue. We utilized a dominant mutant Unstable factor for orange 1-1 (Ufo1-1) which reduces the epigenetic suppression of p1 in various tissues throughout the maize plant. Our proteomic analysis shows how, in the presence of Ufo1-1, key enzymes of the glycolytic and shikimic acid pathways were modulated to produce substrates required for flavonoid synthesis. The finding that the presence of Ufo1-1 affected the expression levels of various enzymes in the lignin pathway was of particular interest. We show that lignin was reduced in Ufo1-1 plants expressing p1 and was associated with the post-transcriptional down regulation of CoA O-methyltransferase (COMT) enzyme. We further correlated the down-regulation of COMT with plant bending phenotype in Ufo1-1 plants expressing p1 and to a stalk lodging phenotype of transgenic p1 plants. This study demonstrates that although there can be adverse consequences to aberrantly overexpressing transcription factors, there might also be benefits such as being able to reduce lignin content for biofuel crops. However, more research will be required to understand the genetic and epigenetic regulation of transcription factors and how their expression can be optimized to obtain desired traits in preferred tissue types. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Michael L Robbins
- Department of Plant Science, The Pennsylvania State University, University Park, PA 16802, USA
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17
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Ma D, Cao W, Kapur A, Felder M, Scarlett CO, Patankar MS, Li L. Differential expression of proteins in naïve and IL-2 stimulated primary human NK cells identified by global proteomic analysis. J Proteomics 2013; 91:151-63. [PMID: 23806757 DOI: 10.1016/j.jprot.2013.06.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/15/2013] [Accepted: 06/17/2013] [Indexed: 12/17/2022]
Abstract
UNLABELLED Natural killer (NK) cells efficiently cytolyse tumors and virally infected cells. Despite the important role that interleukin (IL)-2 plays in stimulating the proliferation of NK cells and increasing NK cell activity, little is known about the alterations in the global NK cell proteome following IL-2 activation. To compare the proteomes of naïve and IL-2-activated primary NK cells and identify key cellular pathways involved in IL-2 signaling, we isolated proteins from naïve and IL-2-activated NK cells from healthy donors, the proteins were trypsinized and the resulting peptides were analyzed by 2D LC ESI-MS/MS followed by label-free quantification. In total, more than 2000 proteins were identified from naïve and IL-2-activated NK cells where 383 proteins were found to be differentially expressed following IL-2 activation. Functional annotation of IL-2 regulated proteins revealed potential targets for future investigation of IL-2 signaling in human primary NK cells. A pathway analysis was performed and revealed several pathways that were not previously known to be involved in IL-2 response, including ubiquitin proteasome pathway, integrin signaling pathway, platelet derived growth factor (PDGF) signaling pathway, epidermal growth factor receptor (EGFR) signaling pathway and Wnt signaling pathway. BIOLOGICAL SIGNIFICANCE The development and functional activity of natural killer (NK) cells is regulated by interleukin (IL)-2 which stimulates the proliferation of NK cells and increases NK cell activity. With the development of IL-2-based immunotherapeutic strategies that rely on the IL-2-mediated activation of NK cells to target human cancers, it is important to understand the global molecular events triggered by IL-2 in human NK cells. The differentially expressed proteins in human primary NK cells following IL-2 activation identified in this study confirmed the activation of JAK-STAT signaling pathway and cell proliferation by IL-2 as expected, but also led to the discovery and identification of other factors that are potentially important in IL-2 signaling. These new factors warrant further investigation on their potential roles in modulating NK cell biology. The results from this study suggest that the activation of NK cells by IL-2 is a dynamic process through which proteins with various functions are regulated. Such findings will be important for the elucidation of molecular pathways involved in IL-2 signaling in NK cells and provide new targets for future studies in NK cell biology.
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18
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Cabrera JA, Butterick TA, Long EK, Ziemba EA, Anderson LB, Duffy CM, Sluiter W, Duncker DJ, Zhang J, Chen Y, Ward HB, Kelly RF, McFalls EO. Reduced expression of mitochondrial electron transport chain proteins from hibernating hearts relative to ischemic preconditioned hearts in the second window of protection. J Mol Cell Cardiol 2013; 60:90-6. [PMID: 23562790 DOI: 10.1016/j.yjmcc.2013.03.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 03/22/2013] [Accepted: 03/23/2013] [Indexed: 10/27/2022]
Abstract
Although protection against necrosis has been observed in both hibernating (HIB) and ischemic preconditioned hearts in the second window of protection (SWOP), a comparison of the mitochondrial proteome between the two entities has not been previously performed. Anesthetized swine underwent instrumentation with a fixed constrictor around the LAD artery and were followed for 12 weeks (HIB; N=7). A second group of anesthetized swine underwent ischemic preconditioning by inflating a balloon within the LAD artery 10 times for 2 min, each separated by 2 min reperfusion and were sacrificed 24h later (SWOP; N=7). Myocardial blood flow and high-energy nucleotides were obtained in the LAD region and normalized to remote regions. Post-sacrifice, protein content as measured with iTRAQ was compared in isolated mitochondria from the LAD area of a Sham heart. Basal regional blood flow in the LAD region when normalized to the remote region was 0.86±0.04 in HIB and 1.02±0.02 in SWOP tissue (P<0.05). Despite reduced regional blood flows in HIB hearts, ATP content in the LAD region, when normalized to the remote region was similar in HIB versus SWOP (1.06±0.06 and 1.02±0.05 respectively; NS) as was the transmural phosphocreatine (PCr) to ATP ratio (2.1±0.2 and 2.2±0.2 respectively; NS). Using iTRAQ, 64 common proteins were identified in HIB and SWOP hearts. Compared with SWOP, the relative abundance of mitochondrial proteins involved with electron transport chain (ETC) were reduced in HIB including NADH dehydrogenase, Cytochrome c reductase and oxidase, ATP synthase, and nicotinamide nucleotide transhydrogenase. Within chronically HIB heart tissue with reduced blood flow, the relative abundance of mitochondrial ETC proteins is decreased when compared with SWOP tissue. These data support the concept that HIB heart tissue subjected to chronically reduced blood flow is associated with a down-regulation in the expression of key mitochondrial proteins involved in electron transport.
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Affiliation(s)
- Jesús A Cabrera
- Cardiology & Cardiothoracic Surgery Sections, VA Medical Center & University of Minnesota, Minneapolis, MN 55417, USA
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Lodha TD, Hembram P, Basak NTJ. Proteomics: A Successful Approach to Understand the Molecular Mechanism of Plant-Pathogen Interaction. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.46149] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Kaltwaßer B, Schulenborg T, Beck F, Klotz M, Schäfer KH, Schmitt M, Sickmann A, Friauf E. Developmental changes of the protein repertoire in the rat auditory brainstem: a comparative proteomics approach in the superior olivary complex and the inferior colliculus with DIGE and iTRAQ. J Proteomics 2012. [PMID: 23201114 DOI: 10.1016/j.jprot.2012.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Protein profiles of developing neural circuits undergo manifold changes. The aim of this proteomic analysis was to quantify postnatal changes in two auditory brainstem areas in a comparative approach. Protein samples from the inferior colliculus (IC) and the superior olivary complex (SOC) were obtained from neonatal (P4) and young adult (P60) rats. The cytosolic fractions of both areas were examined by 2-D DIGE, and the plasma membrane-enriched fraction of the IC was analyzed via iTRAQ. iTRAQ showed a regulation in 34% of the quantified proteins. DIGE revealed 12% regulated spots in both the SOC and IC and, thus, numeric congruency. Although regulation in KEGG pathways displayed a similar pattern in both areas, only 13 of 71 regulated DIGE proteins were regulated in common, implying major area-specific differences. 89% of regulated glycolysis/gluconeogenesis and citrate cycle proteins were up-regulated in the SOC or IC, suggesting a higher energy demand in adulthood. Seventeen cytoskeleton proteins were regulated, consistent with complex morphological reorganization between P4 and P60. Fourteen were uniquely regulated in the SOC, providing further evidence for area-specific differences. Altogether, we provide the first elaborate catalog of proteins involved in auditory brainstem development, several of them possibly of particular developmental relevance.
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Affiliation(s)
- Bernd Kaltwaßer
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
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21
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Cabrera JA, Ziemba EA, Colbert R, Anderson LB, Sluiter W, Duncker DJ, Butterick TA, Sikora J, Ward HB, Kelly RF, McFalls EO. Altered expression of mitochondrial electron transport chain proteins and improved myocardial energetic state during late ischemic preconditioning. Am J Physiol Heart Circ Physiol 2012; 302:H1974-82. [PMID: 22389388 DOI: 10.1152/ajpheart.00372.2011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Altered expression of mitochondrial electron transport proteins has been shown in early preconditioned myocardial tissue. We wished to determine whether these alterations persist in the Second Window of Protection (SWOP) and if so, whether a favorable energetic state is facilitated during subsequent ischemia. Fourteen pigs underwent a SWOP protocol with ten 2-minute balloon inflations in the LAD artery, each separated by 2 minutes reperfusion. Twenty-four hours later, mitochondria were isolated from SWOP and SHAM pig hearts and analyzed for uncoupling protein (UCP)-2 content by western blot analysis, proteomic changes by iTRAQ(®) and respiration by an oxygen electrode. In parallel in vivo studies, high-energy nucleotides were obtained by transmural biopsy from anesthetized SWOP and SHAM pigs at baseline and during sustained low-flow ischemia. Compared with SHAM mitochondria, ex vivo SWOP heart tissue demonstrated increased expression of UCP-2, Complex IV (cytochrome c oxidase) and Complex V (ATPase) proteins. In comparison with SHAM pigs during in vivo conditions, transmural energetics in SWOP hearts, as estimated by the free energy of ATP hydrolysis (ΔG(0)), were similar at baseline but had decreased by the end of low-flow ischemia (-57.0 ± 2.1 versus -51.1 ± 1.4 kJ/mol; P < 0.05). In conclusion, within isolated mitochondria from preconditioned SWOP hearts, UCP-2 is increased and in concert with enhanced Complex IV and V proteins, imparts a favorable energetic state during low-flow ischemia. These data support the notion that mitochondrial adaptations that may reduce oxidant damage do not reduce the overall efficiency of energetics during sustained oxygen deprivation.
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Affiliation(s)
- Jesús A Cabrera
- Cardiology and Cardiothoracic Surgery Sections, VA Medical Center, University of Minnesota, Minneapolis, MN 55417, USA
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22
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Jardin J, Mollé D, Piot M, Lortal S, Gagnaire V. Quantitative proteomic analysis of bacterial enzymes released in cheese during ripening. Int J Food Microbiol 2012; 155:19-28. [PMID: 22305888 DOI: 10.1016/j.ijfoodmicro.2012.01.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 12/23/2011] [Accepted: 01/07/2012] [Indexed: 11/28/2022]
Abstract
Due to increasingly available bacterial genomes in databases, proteomic tools have recently been used to screen proteins expressed by micro-organisms in food in order to better understand their metabolism in situ. While the main objective is the systematic identification of proteins, the next step will be to bridge the gap between identification and quantification of these proteins. For that purpose, a new mass spectrometry-based approach was applied, using isobaric tagging reagent for quantitative proteomic analysis (iTRAQ), which are amine specific and yield labelled peptides identical in mass. Experimental Swiss-type cheeses were manufactured from microfiltered milk using Streptococcus thermophilus ITG ST20 and Lactobacillus helveticus ITG LH1 as lactic acid starters. At three ripening times (7, 20 and 69 days), cheese aqueous phases were extracted and enriched in bacterial proteins by fractionation. Each sample, standardised in protein amount prior to proteomic analyses, was: i) analysed by 2D-electrophoresis for qualitative analysis and ii) submitted to trypsinolysis, and labelled with specific iTRAQ tag, one per ripening time. The three labelled samples were mixed together and analysed by nano-LC coupled on-line with ESI-QTOF mass spectrometer. Thirty proteins, both from bacterial or bovine origin, were identified and efficiently quantified. The free bacterial proteins detected were enzymes from the central carbon metabolism as well as stress proteins. Depending on the protein considered, the quantity of these proteins in the cheese aqueous extract increased from 2.5 to 20 fold in concentration from day 7 to day 69 of ripening.
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Affiliation(s)
- Julien Jardin
- INRA, UMR1253, Science et Technologie du lait et de l'Œuf, Rennes, France
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Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, remains one of the most prevalent human pathogens in the world. Knowledge regarding the bacilli's physiology as well as its mechanisms of virulence, immunogenicity, and pathogenesis has increased greatly in the last three decades. However, the function of about one-quarter of the Mtb coding genome and the precise activity and protein networks of most of the Mtb proteins are still unknown. Protein mass spectrometry and a new interest in research toward the field of functional proteomics have given a new light to the study of this bacillus and will be the focus of this review. We will also discuss new perspectives in the proteomics field, in particular targeted mass spectrometry methods and their potential applications in TB research and discovery.
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Affiliation(s)
- M Carolina Mehaffy
- Department of Microbiology, Immunology and Pathology, Colorado State University, 1619 Campus Delivery, Fort Collins, Colorado 80523, United States
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Abstract
Defining the plasma membrane proteome is crucial to understand the role of plasma membrane in fundamental biological processes. Change in membrane proteins is one of the first events that take place under pathological conditions, making plasma membrane proteins a likely source of potential disease biomarkers with prognostic or diagnostic potential. Membrane proteins are also potential targets for monoclonal antibodies and other drugs that block receptors or inhibit enzymes essential to the disease progress. Despite several advanced methods recently developed for the analysis of hydrophobic proteins and proteins with posttranslational modifications, integral membrane proteins are still under-represented in plasma membrane proteome. Recent advances in proteomic investigation of plasma membrane proteins, defining their roles as diagnostic and prognostic disease biomarkers and as target molecules in disease treatment, are presented.
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Affiliation(s)
- Marijana Rucevic
- COBRE Center for Cancer Research Development, Rhode Island Hospital, Providence, RI, USA
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25
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Zhou X, He Z, Henegar J, Allen B, Bigler S. Expression of allograft inflammatory factor-1 (AIF-1) in acute cellular rejection of cardiac allografts. Cardiovasc Pathol 2011; 20:e177-84. [DOI: 10.1016/j.carpath.2010.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 07/27/2010] [Accepted: 08/09/2010] [Indexed: 11/18/2022] Open
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26
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Holland M, Castro FV, Alexander S, Smith D, Liu J, Walker M, Bitton D, Mulryan K, Ashton G, Blaylock M, Bagley S, Connolly Y, Bridgeman J, Miller C, Krishnan S, Dempsey C, Masurekar A, Stern P, Whetton A, Saha V. RAC2, AEP, and ICAM1 expression are associated with CNS disease in a mouse model of pre-B childhood acute lymphoblastic leukemia. Blood 2011; 118:638-49. [PMID: 21606482 DOI: 10.1182/blood-2010-09-307330] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We developed a murine model of CNS disease to obtain a better understanding of the pathogenesis of CNS involvement in pre-B-cell acute lymphoblastic leukemia (ALL). Semiquantitative proteomic discovery-based approaches identified unique expression of asparaginyl endopeptidase (AEP), intercellular adhesion molecule 1 (ICAM1), and ras-related C3 botulinum toxin substrate 2 (RAC2), among others, in an invasive pre-B-cell line that produced CNS leukemia in NOD-SCID mice. Targeting RAC2 significantly inhibited in vitro invasion and delayed disease onset in mice. Induced expression of RAC2 in cell lines with low/absent expression of AEP and ICAM1 did not result in an invasive phenotype or murine CNS disease. Flow cytometric analysis identified an enriched population of blast cells expressing ICAM1/lymphocyte function associated antigen-1 (LFA-1)/CD70 in the CD10(+)/CD19(+) fraction of bone marrow aspirates obtained from relapsed compared with normal controls and those with primary disease. CD10(+)/CD19(+) fractions obtained from relapsed patients also express RAC2 and give rise to CNS disease in mice. Our data suggest that combinations of processes are involved in the pathogenesis of CNS disease in pre-B-cell ALL, support a model in which CNS disease occurs as a result of external invasion, and suggest that targeting the processes of adhesion and invasion unique to pre-B cells may prevent recurrences within the CNS.
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Affiliation(s)
- Mark Holland
- Cancer Research UK Children's Cancer Group, Manchester Academic Health Science Centre, School of Cancer & Enabling Sciences, University of Manchester, Manchester, United Kingdom
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27
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Colucci-D'Amato L, Farina A, Vissers JPC, Chambery A. Quantitative neuroproteomics: classical and novel tools for studying neural differentiation and function. Stem Cell Rev Rep 2011; 7:77-93. [PMID: 20352529 DOI: 10.1007/s12015-010-9136-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mechanisms underlying neural stem cell proliferation, differentiation and maturation play a critical role in the formation and wiring of neuronal connections. This process involves the activation of multiple serial events, which guide the undifferentiated cells to different lineages via distinctive developmental programs, forming neuronal circuits and thus shaping the adult nervous system. Furthermore, alterations within these strictly regulated pathways can lead to severe neurological and psychiatric diseases. In this framework, the investigation of the high dynamic protein expression changes and other factors affecting protein functions, for example post-translational modifications, the alterations of protein interaction networks, is of pivotal importance for the understanding of the molecular mechanisms responsible for cell differentiation. More recently, proteomic studies in neuroscience ("neuroproteomics") are receiving increased interest for the primary understanding of the regulatory networks underlying neuronal differentiation processes. Besides the classical two-dimensional-based proteomic strategies, the emerging platforms for LC-MS shotgun proteomic analysis hold great promise in unraveling the molecular basis of neural stem cell differentiation. In this review, recent advancements in label-free LC-MS quantitative neuroproteomics are highlighted as a new tool for the study of neural differentiation and functions, in comparison to mass spectrometry-based labeling approaches. The more commonly used protein profiling strategies and model systems for the analysis of neural differentiation are also discussed, along with the challenging proteomic approaches aimed to analyze the nervous system-specific organelles, the neural cells secretome and the specific protein interaction networks.
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Affiliation(s)
- Luca Colucci-D'Amato
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
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Abstract
Membrane proteins are key molecules in the cell and are important targets for drug development. Much effort has, therefore, been directed towards research of this group of proteins, but their hydrophobic nature can make working with them challenging. Here we discuss methodologies used in the study of the membrane proteome, specifically discussing approaches that circumvent technical issues specific to the membrane. In addition, we review several techniques used for visualization, qualification, quantitation and localization of membrane proteins. The combination of the techniques we describe holds great promise to allow full characterization of the membrane proteome and to map the dynamic changes within it essential for cellular function.
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Affiliation(s)
- Arnoud J Groen
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
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Abstract
Proteomics is the study of global gene expression of an organ, body system, fluid, or cellular compartment at the protein level. Proteomic findings are reflective of complex gene × environment interactions, and the importance of this is increasingly appreciated in schizophrenia research. In this review, we outline the main proteomic methods available to researchers in this area and summarize, for the first time, the findings of the main quantitative neuroproteomic investigations of schizophrenia brain. Our review of these data revealed 16 gray matter proteins, and eight white matter proteins that were differentially expressed in the same direction in two or more investigations. Pathway analysis identified cellular assembly and organization as particularly disrupted in both gray and white matter, whereas the glycolysis-gluconeogenesis pathway was the major signaling pathway significantly altered in both. Reassuringly, these findings show remarkable convergence with functional pathways and positional candidate genes implicated from genomic studies. The specificity of schizophrenia proteomic findings are also addressed in the context of neuroproteomic investigations of neurodegenerative disorders and bipolar disorder. Finally, we discuss the major challenges in the field of neuroproteomics, such as the need for high throughput validation methods and optimal sample preparation. Future directions in the neuroproteomics of schizophrenia, including the use of blood-based biomarker work, the need to focus on subproteomes, and the increasing use of mass spectrometry-based methods are all discussed. This area of research is still in its infancy and offers huge potential to our understanding of schizophrenia on a cellular level.
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Affiliation(s)
- Jane A English
- Proteome Research Centre, UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, and Medical Sciences, University College Dublin, Ireland
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Kelly RF, Cabrera JA, Ziemba EA, Crampton M, Anderson LB, McFalls EO, Ward HB. Continued depression of maximal oxygen consumption and mitochondrial proteomic expression despite successful coronary artery bypass grafting in a swine model of hibernation. J Thorac Cardiovasc Surg 2011; 141:261-8. [DOI: 10.1016/j.jtcvs.2010.08.061] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Revised: 08/20/2010] [Accepted: 08/27/2010] [Indexed: 10/18/2022]
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Miike K, Aoki M, Yamashita R, Takegawa Y, Saya H, Miike T, Yamamura KI. Proteome profiling reveals gender differences in the composition of human serum. Proteomics 2010; 10:2678-91. [PMID: 20480504 DOI: 10.1002/pmic.200900496] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Proteome analysis using human serum is a technological advancement that will enable the discovery of novel biomarkers and biomarker patterns of various human diseases. Although proteome analysis using serum has potential in disease prevention, early diagnosis and treatment of diseases, and evaluation of pharmacotherapies, this technology is still in its infancy. Thus, we sought to develop an advanced method of conducting proteome analysis on human serum. In this study, we report the development of the semi-comprehensive protein analytical technique, which involves the systematic use of iTRAQ labeling, HPLC, nano-LC and MS. We compared the composition of the serum proteome in males and females using this technique and detected gender-based differences in serum protein composition. This technology will enable the generation of databases that may ultimately lead to the discovery of specific biomarkers or biomarker patterns of various diseases.
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Affiliation(s)
- Koichiro Miike
- Department of Child Development, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University Graduate School, Kumamoto, Japan
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32
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Abstract
Oxidative stress and protein carbonylation is implicated in aging and various diseases such as neurodegenerative disorders, diabetes, and cancer. Therefore, the accurate identification and quantification of protein carbonylation may lead to the discovery of new biomarkers. We have developed a new method that combines avidin affinity selection of carbonylated proteins with iTRAQ labeling and LC fractionation of intact proteins. This simple LC-based workflow is an effective technique to reduce sample complexity, minimize technical variation, and enable simultaneous quantification of four samples. This method was used to determine protein oxidation in an iron accumulating mutant of Saccharomyces cerevisiae exposed to oxidative stress. Overall, 31 proteins were identified with 99% peptide confidence, and of those, 27 proteins were quantified. Most of the identified proteins were associated with energy metabolism (32.3%), and cellular defense, transport, and folding (38.7%), suggesting a drop in energy production and reducing power of the cells due to the damage of glycolytic enzymes and decrease in activity of enzymes involved in protein protection and regeneration. In addition, the oxidation sites of seven proteins were identified and their estimated position also indicated a potential impact on the enzymatic activities. Predicted 3D structures of peroxiredoxin (TSA1) and thioredoxin II (TRX2) revealed close proximity of all oxidized amino acid residues to the protein active sites.
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Affiliation(s)
- Jin-Hee Kim
- Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - Miroslav Sedlak
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana
| | - Qiang Gao
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - Catherine P. Riley
- Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
| | - Fred E. Regnier
- Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - Jiri Adamec
- Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
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Serrano J, Higgins Ln, Witthuhn BA, Anderson LB, Markowski T, Holcombe GW, Kosian PA, Korte JJ, Tietge JE, Degitz SJ. In vivo assessment and potential diagnosis of xenobiotics that perturb the thyroid pathway: Proteomic analysis of Xenopus laevis brain tissue following exposure to model T4 inhibitors. Comp Biochem Physiol Part D Genomics Proteomics 2010; 5:138-50. [PMID: 20452843 DOI: 10.1016/j.cbd.2010.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 03/24/2010] [Accepted: 03/25/2010] [Indexed: 02/08/2023]
Abstract
As part of a multi-endpoint systems approach to develop comprehensive methods for assessing endocrine stressors in vertebrates, differential protein profiling was used to investigate expression patterns in the brain of the amphibian model (Xenopus laevis) following in vivo exposure to a suite of T4 synthesis inhibitors. We specifically address the application of Two Dimensional Polyacrylamide Gel Electrophoresis (2D PAGE), Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) and LC-MS/MS to assess changes in relative protein expression levels. 2D PAGE and iTRAQ proved to be effective complementary techniques for distinguishing protein changes in the developing amphibian brain in response to T4 synthesis inhibition. This information served to evaluate the use of distinctive protein profiles as a potential mechanism to screen chemicals for endocrine activity in anurans. Regulatory pathways associated with proteins expressed as a result of chemical effect are reported. To our knowledge, this is also the first account of the anuran larvae brain proteome characterization using proteomic technologies. Correlation of protein changes to other cellular and organism-level responses will aid in the development of a more rapid and cost-effective, non-mammalian screening assay for thyroid axis-disrupting chemicals.
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Sanchez-Niño MD, Sanz AB, Lorz C, Gnirke A, Rastaldi MP, Nair V, Egido J, Ruiz-Ortega M, Kretzler M, Ortiz A. BASP1 promotes apoptosis in diabetic nephropathy. J Am Soc Nephrol 2010; 21:610-21. [PMID: 20110383 DOI: 10.1681/asn.2009020227] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Apoptosis contributes to the development of diabetic nephropathy (DN), but the mechanisms that lead to diabetes-induced cell death are not fully understood. Here, we combined a functional genomics screen for cDNAs that induce apoptosis in vitro with transcriptional profiling of renal biopsies from patients with DN. Twelve of the 138 full-length cDNAs that induced cell death in human embryonic kidney cells matched upregulated mRNA transcripts in tissue from human DN. Confirmatory screens identified induction of BASP1 in tubular cross sections of human DN tissue. In vitro, apoptosis-inducing conditions such as serum deprivation, high concentrations of glucose, and proinflammatory cytokines increased BASP1 mRNA and protein in human tubular epithelial cells. In normal cells, BASP1 localized to the cytoplasm, but in apoptotic cells, it colocalized with actin in the periphery. Overexpression of BASP1 induced cell death with features of apoptosis; conversely, small interfering RNA (siRNA)-mediated knockdown of BASP1 protected tubular cells from apoptosis. Supporting possible involvement of BASP1 in renal disease other than DN, we also observed significant upregulation of renal BASP1 in spontaneously hypertensive rats and a trend toward increased tubulointerstitial BASP1 mRNA in human hypertensive nephropathy. In summary, a combined functional genomics approach identified BASP1 as a proapoptotic factor in DN and possibly also in hypertensive nephropathy.
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Affiliation(s)
- Maria Dolores Sanchez-Niño
- Nefrología, Fundación Jiménez Díaz, Universidad Autonoma de Madrid and Instituto Reina Sofia de Investigaciones Nefrológicas-IRSIN, Madrid, Spain
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Abstract
Natural killer (NK) cells, a prominent component of the innate immune system, are large granular lymphocytes that respond rapidly to a variety of insults via cytokine secretion and cytolytic activity. Recently, there has been growing insight into the biological functions of NK cells, in particular into their roles in infection, tumorurveillance and autoimmunity. Under these pathophysiological circumstances, NK cells readily home to the central nervous system (CNS) tissues to combat infection and presumably to curb progression of tumor. Bystander neuronal and/or glial cell damage can occur in this setting. Paradoxically, NK cells appear to have an inhibitory role for autoimmune responses within the CNS. As in the periphery, NK cells act in concert with T cells and other lymphocytes responsible for CNS pathology and immune regulation. Insights into the molecular signals and pathways governing the diverse biological effects of NK cells are keys for designing NK cell-based therapy for CNS infections, tumor and autoimmune diseases.NK cells readily accumulate in homing to CNS tissues under the pathophysiological situations. This process is tightly controlled by a number of chemokines and chemokine receptors. There is ample of evidence that NK cells within the CNS contribute to the control of infections and might limit progression of certain tumor. Bystander neuronal and/or glial cell damage can occur. In certain autoimmune conditions of the CNS, NK cells appear to have an inhibitory role. Disassociation of disease-inhibiting versus disease-promoting effects of NK cells is a key to harnessing NK cells for therapeutic purposes. To achieve this goal, a generation of genetic models with selective NK cell deficiency, and development of reagents (antibodies) for visualizing subsets of NK cells in situ will be necessary.
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Chandramouli K, Qian PY. Proteomics: challenges, techniques and possibilities to overcome biological sample complexity. Hum Genomics Proteomics 2009; 2009. [PMID: 20948568 PMCID: PMC2950283 DOI: 10.4061/2009/239204] [Citation(s) in RCA: 219] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 08/28/2009] [Indexed: 01/12/2023]
Abstract
Proteomics is the large-scale study of the structure and function of proteins in complex biological sample. Such an approach has the potential value to understand the complex nature of the organism. Current proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of proteome. Advances in protein fractionation and labeling techniques have improved protein identification to include the least abundant proteins. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. However, the major limitation of proteomic investigations remains the complexity of biological structures and physiological processes, rendering the path of exploration paved with various difficulties and pitfalls. The quantity of data that is acquired with new techniques places new challenges on data processing and analysis. This article provides a brief overview of currently available proteomic techniques and their applications, followed by detailed description of advantages and technical challenges. Some solutions to circumvent technical difficulties are proposed.
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Riedl MS, Braun PD, Kitto KF, Roiko SA, Anderson LB, Honda CN, Fairbanks CA, Vulchanova L. Proteomic analysis uncovers novel actions of the neurosecretory protein VGF in nociceptive processing. J Neurosci 2009; 29:13377-88. [PMID: 19846725 DOI: 10.1523/JNEUROSCI.1127-09.2009] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Peripheral tissue injury is associated with changes in protein expression in sensory neurons that may contribute to abnormal nociceptive processing. We used cultured dorsal root ganglion (DRG) neurons as a model of axotomized neurons to investigate early changes in protein expression after nerve injury. Comparing protein levels immediately after DRG dissociation and 24 h later by proteomic differential expression analysis, we found a substantial increase in the levels of the neurotrophin-inducible protein VGF (nonacronymic), a putative neuropeptide precursor. In a rodent model of nerve injury, VGF levels were increased within 24 h in both injured and uninjured DRG neurons, and the increase persisted for at least 7 d. VGF was also upregulated 24 h after hindpaw inflammation. To determine whether peptides derived from proteolytic processing of VGF participate in nociceptive signaling, we examined the spinal effects of AQEE-30 and LQEQ-19, potential proteolytic products shown previously to be bioactive. Each peptide evoked dose-dependent thermal hyperalgesia that required activation of the mitogen-activated protein kinase p38. In addition, LQEQ-19 induced p38 phosphorylation in spinal microglia when injected intrathecally and in the BV-2 microglial cell line when applied in vitro. In summary, our results demonstrate rapid upregulation of VGF in sensory neurons after nerve injury and inflammation and activation of microglial p38 by VGF peptides. Therefore, VGF peptides released from sensory neurons may participate in activation of spinal microglia after peripheral tissue injury.
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Armenta JM, Hoeschele I, Lazar IM. Differential protein expression analysis using stable isotope labeling and PQD linear ion trap MS technology. J Am Soc Mass Spectrom 2009; 20:1287-1302. [PMID: 19345114 DOI: 10.1016/j.jasms.2009.02.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/19/2009] [Accepted: 02/21/2009] [Indexed: 05/27/2023]
Abstract
An isotope tags for relative and absolute quantitation (iTRAQ)-based reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) method was developed for differential protein expression profiling in complex cellular extracts. The estrogen positive MCF-7 cell line, cultured in the presence of 17beta-estradiol (E2) and tamoxifen (Tam), was used as a model system. MS analysis was performed with a linear trap quadrupole (LTQ) instrument operated by using pulsed Q dissociation (PQD) detection. Optimization experiments were conducted to maximize the iTRAQ labeling efficiency and the number of quantified proteins. MS data filtering criteria were chosen to result in a false positive identification rate of <4%. The reproducibility of protein identifications was approximately 60%-67% between duplicate, and approximately 50% among triplicate LC-MS/MS runs, respectively. The run-to-run reproducibility, in terms of relative standard deviations (RSD) of global mean iTRAQ ratios, was better than 10%. The quantitation accuracy improved with the number of peptides used for protein identification. From a total of 530 identified proteins (P < 0.001) in the E2/Tam treated MCF-7 cells, a list of 255 proteins (quantified by at least two peptides) was generated for differential expression analysis. A method was developed for the selection, normalization, and statistical evaluation of such datasets. An approximate approximately 2-fold change in protein expression levels was necessary for a protein to be selected as a biomarker candidate. According to this data processing strategy, approximately 16 proteins involved in biological processes such as apoptosis, RNA processing/metabolism, DNA replication/transcription/repair, cell proliferation and metastasis, were found to be up- or down-regulated.
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Affiliation(s)
- Jenny M Armenta
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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Liumbruno G, D'Alessandro A, Grazzini G, Zolla L. Blood-related proteomics. J Proteomics 2010; 73:483-507. [PMID: 19567275 DOI: 10.1016/j.jprot.2009.06.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 06/17/2009] [Accepted: 06/20/2009] [Indexed: 12/12/2022]
Abstract
Blood-related proteomics is an emerging field, recently gaining momentum. Indeed, a wealth of data is now available and a plethora of groups has contributed to add pieces to the jigsaw puzzle of protein complexity within plasma and blood cells. In this review article we purported to sail across the mare magnum of the actual knowledge in this research endeavour. The main strides in proteomic investigations on red blood cells, platelets, plasma and white blood cells are hereby presented in a chronological order. Moreover, a glance is given at prospective studies which promise to shift the focus of attention from the end product to its provider, the donor, in a sort of Kantian "Copernican revolution". A well-rounded portrait of the usefulness of proteomics in blood-related research is accurately given. In particular, proteomic tools could be adopted to follow the main steps of the blood-banking production processes (a comparison of collection methods, pathogen inactivation techniques, storage protocols). Thus proteomics has been recently transformed from a mere basic-research extremely-expensive toy into a dramatically-sensitive and efficient eye-lens to either delve into the depths of the molecular mechanisms of blood and blood components or to establish quality parameters in the blood-banking production chain totally anew.
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Gagnaire V, Jardin J, Jan G, Lortal S. Invited review: Proteomics of milk and bacteria used in fermented dairy products: From qualitative to quantitative advances. J Dairy Sci 2009; 92:811-25. [DOI: 10.3168/jds.2008-1476] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Shui W, Gilmore SA, Sheu L, Liu J, Keasling JD, Bertozzi CR. Quantitative proteomic profiling of host-pathogen interactions: the macrophage response to Mycobacterium tuberculosis lipids. J Proteome Res 2009; 8:282-9. [PMID: 19053526 DOI: 10.1021/pr800422e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis) is an intracellular pathogen possessing a complex mixture of cell wall lipids that are thought to modulate the activities of host macrophages. In this study, we employed two state-of-the-art quantitative proteomic approaches, metabolic labeling SILAC and chemical isobaric tagging iTRAQ, to study changes in macrophage protein expression in response to exposure to M. tuberculosis lipids. From a total of 1286 proteins identified, 463 were discovered by both isotope-labeling strategies at a high consistency, and the rest of proteins were detected by only one of the two approaches. Upon exposure to mycobacterial cell wall lipids, 166 macrophage proteins showed differential expression. These included proteins involved in the immune response, oxidation and reduction, and vesicle transport, as well as other cellular processes. The response of the macrophage proteome to M. tuberculosis lipids reflects the cell's innate defense mechanisms as well as lipid-induced processes that may benefit the pathogen.
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Affiliation(s)
- Wenqing Shui
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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43
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Abstract
Shotgun proteomics involves the analysis of peptides obtained by enzymatic digestions of proteins and subsequent identification via tandem mass spectrometry. This approach is an effective method for studying global protein expression in neuronal systems. The method described here is a quantitative shotgun neuroproteomics method using amine-specific isobaric tags for a relative and absolute quantitation (iTRAQ)-based workflow. We will provide the technical details for sample preparation, two-dimensional liquid chromatography, tandem mass spectrometry, database search, and statistical analysis to identify differentially expressed proteins. We will use a recent study on a rat model of multiple sclerosis, experimental autoimmune encephalomyelitis to illustrate the successful application of this method.
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Affiliation(s)
| | | | - Hong Li
- Address correspondence to:Hong Li, Department of Biochemistry and Molecular Biology, UMDNJ-NJMS, 185 S. Orange Ave. MSB E-609, Newark, NJ 07103. Tel: 973-972-8396, Fax: 973-972-5594,
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Han CL, Chien CW, Chen WC, Chen YR, Wu CP, Li H, Chen YJ. A Multiplexed Quantitative Strategy for Membrane Proteomics. Mol Cell Proteomics 2008; 7:1983-97. [DOI: 10.1074/mcp.m800068-mcp200] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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45
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Gundry RL, Boheler KR, Van Eyk JE, Wollscheid B. A novel role for proteomics in the discovery of cell-surface markers on stem cells: Scratching the surface. Proteomics Clin Appl 2008; 2:892-903. [PMID: 19526049 DOI: 10.1002/prca.200780122] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The concept of cell-based therapy has been advocated as a novel approach for treating diseases or conditions where regeneration of cells, tissue and/or potentially organs is required. A promising source for cell-replacement therapies is provided by stem cells, but the success of this approach will ultimately rely on the ability to isolate primary stem or progenitor cells. Cell-surface protein markers will play a critical role in this step. Current methodologies for the identification of cell-surface protein markers rely primarily on antibody availability and flow cytometry, but many cell-surface proteins remain undetectable. Proteomic technologies now offer the possibility to specifically identify and investigate the cell-surface subproteome in a quantitative and discovery-driven manner. Once a cell surface protein marker panel has been identified by MS and the antibodies become available, the panel should permit the identification, tracking, and/or isolation of stem or progenitor cells that may be appropriate for therapeutics. This review provides a context for the use of proteomics in discovering new cell-surface markers for stem cells.
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Affiliation(s)
- Rebekah L Gundry
- Johns Hopkins School of Medicine, Department of Medicine, Baltimore, MD, USA
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46
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Griffin TJ, Xie H, Bandhakavi S, Popko J, Mohan A, Carlis JV, Higgins L. iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer. J Proteome Res 2007; 6:4200-9. [PMID: 17902639 PMCID: PMC2533114 DOI: 10.1021/pr070291b] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
For proteomic analysis using tandem mass spectrometry, linear ion trap instruments provide unsurpassed sensitivity but unreliably detect low mass peptide fragments, precluding their use with iTRAQ reagent-labeled samples. Although the popular LTQ linear ion trap supports analyzing iTRAQ reagent-labeled peptides via pulsed Q dissociation, PQD, its effectiveness remains questionable. Using a standard mixture, we found careful tuning of relative collision energy necessary for fragmenting iTRAQ reagent-labeled peptides, and increasing microscan acquisition and repeat count improves quantification but identifies somewhat fewer peptides. We developed software to calculate abundance ratios via summing reporter ion intensities across spectra matching to each protein, thereby providing maximized accuracy. Testing found that results closely corresponded between analysis using optimized LTQ-PQD settings plus our software and using a Qstar instrument. Thus, we demonstrate the effectiveness of LTQ-PQD analyzing iTRAQ reagent-labeled peptides, and provide guidelines for successful quantitative proteomic studies.
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Affiliation(s)
- Timothy J Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, Center for Mass Spectrometry and Proteomics, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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Abstract
Membrane proteins are critical for normal cellular differentiation and function, and alterations in these proteins often leads to cell dysfunction and disease. Membrane proteomics aims to identify the membrane protein constituents, their posttranslational modifications, protein-protein interactions, and dynamics. Efforts to identify membrane proteins and elucidate their dynamics have been plagued by the challenges presented by studying water insoluble proteins that are distributed among a range of membranes in a cell and often occur at a relatively low abundance. This brief review presents a summary of the literature related to membrane proteomics with an emphasis on efforts to develop effective protocols for the enrichment of membrane proteins, particularly those located in the plasma membrane.
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Affiliation(s)
- Bruce A Macher
- Department of Chemistry and Biochemistry, 1600 Holloway Ave., San Francisco State University, San Francisco, CA 94132, USA.
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Affiliation(s)
- Anna E Speers
- Department of Pharmacology, University of Colorado School of Medicine, P.O. Box 6511, MS 8303, Aurora, Colorado 80045, USA
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