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Vujicic I, Rusevski A, Stankov O, Popov Z, Dimovski A, Davalieva K. Potential Role of Seven Proteomics Tissue Biomarkers for Diagnosis and Prognosis of Prostate Cancer in Urine. Diagnostics (Basel) 2022; 12:diagnostics12123184. [PMID: 36553191 PMCID: PMC9777474 DOI: 10.3390/diagnostics12123184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
As the currently available tests for the clinical management of prostate cancer (PCa) are still far from providing precise diagnosis and risk stratification, the identification of new molecular marker(s) remains a pertinent clinical need. Candidate PCa biomarkers from the published proteomic comparative studies of prostate tissue (2002-2020) were collected and systematically evaluated. AZGP1, MDH2, FABP5, ENO1, GSTP1, GSTM2, and EZR were chosen for further evaluation in the urine of 85 PCa patients and controls using ELISA. Statistically significant differences in protein levels between PCa and BPH showed FABP5 (p = 0.019) and ENO1 (p = 0.015). A biomarker panel based on the combination of FABP5, ENO1, and PSA provided the highest accuracy (AUC = 0.795) for PCa detection. The combination of FABP5, EZR, AZGP1, and MDH2 showed AUC = 0.889 in PCa prognosis, with 85.29% of the samples correctly classified into low and high Gleason score (GS) groups. The addition of PSA to the panel slightly increased the AUC to 0.914. AZGP1, FABP5, and EZR showed significant correlation with GS, stage, and percentage of positive biopsy cores. Although validation using larger patient cohorts will be necessary to establish the credibility of the proposed biomarker panels in a clinical context, this study opens a way for the further testing of more high-quality proteomics biomarkers, which could ultimately add value to the clinical management of PCa.
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Affiliation(s)
- Ivo Vujicic
- University Clinic for Urology, University Clinical Centre “Mother Theresa”, 1000 Skopje, North Macedonia
| | - Aleksandar Rusevski
- Research Centre for Genetic Engineering and Biotechnology “Georgi D Efremov”, Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia
| | - Oliver Stankov
- University Clinic for Urology, University Clinical Centre “Mother Theresa”, 1000 Skopje, North Macedonia
| | - Zivko Popov
- Clinical Hospital “Acibadem Sistina”, 1000 Skopje, North Macedonia
- Medical Faculty, University “St. Cyril and Methodius”, 1000 Skopje, North Macedonia
- Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia
| | - Aleksandar Dimovski
- Research Centre for Genetic Engineering and Biotechnology “Georgi D Efremov”, Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia
- Faculty of Pharmacy, University “St. Cyril and Methodius”, 1000 Skopje, North Macedonia
| | - Katarina Davalieva
- Research Centre for Genetic Engineering and Biotechnology “Georgi D Efremov”, Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia
- Correspondence:
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Gao ZF, Shen Z, Chao Q, Yan Z, Ge XL, Lu T, Zheng H, Qian CR, Wang BC. Large-scale Proteomic and Phosphoproteomic Analyses of Maize Seedling Leaves During De-etiolation. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:397-414. [PMID: 33385613 PMCID: PMC8242269 DOI: 10.1016/j.gpb.2020.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/16/2019] [Accepted: 05/12/2020] [Indexed: 12/20/2022]
Abstract
De-etiolation consists of a series of developmental and physiological changes that a plant undergoes in response to light. During this process light, an important environmental signal, triggers the inhibition of mesocotyl elongation and the production of photosynthetically active chloroplasts, and etiolated leaves transition from the "sink" stage to the "source" stage. De-etiolation has been extensively studied in maize (Zea mays L.). However, little is known about how this transition is regulated. In this study, we described a quantitative proteomic and phosphoproteomic atlas of the de-etiolation process in maize. We identified 16,420 proteins in proteome, among which 14,168 proteins were quantified. In addition, 8746 phosphorylation sites within 3110 proteins were identified. From the combined proteomic and phosphoproteomic data, we identified a total of 17,436 proteins. Only 7.0% (998/14,168) of proteins significantly changed in abundance during de-etiolation. In contrast, 26.6% of phosphorylated proteins exhibited significant changes in phosphorylation level; these included proteins involved in gene expression and homeostatic pathways and rate-limiting enzymes involved in photosynthetic light and carbon reactions. Based on phosphoproteomic analysis, 34.0% (1057/3110) of phosphorylated proteins identified in this study contained more than 2 phosphorylation sites, and 37 proteins contained more than 16 phosphorylation sites, indicating that multi-phosphorylation is ubiquitous during the de-etiolation process. Our results suggest that plants might preferentially regulate the level of posttranslational modifications (PTMs) rather than protein abundance for adapting to changing environments. The study of PTMs could thus better reveal the regulation of de-etiolation.
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Affiliation(s)
- Zhi-Fang Gao
- Key Laboratory of Photobiology, CAS, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Shen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Qing Chao
- Key Laboratory of Photobiology, CAS, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhen Yan
- Key Laboratory of Photobiology, CAS, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan-Liang Ge
- Institute of Crop Cultivation and Farming, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Tiancong Lu
- Beijing ProteinWorld Biotech, Beijing 100012, China
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Biological Mass Spectrometry Facility, Rutgers University, Piscataway, NJ 08855, USA
| | - Chun-Rong Qian
- Institute of Crop Cultivation and Farming, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Bai-Chen Wang
- Key Laboratory of Photobiology, CAS, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Single-Cell RNA Sequencing Reveals that the Switching of the Transcriptional Profiles of Cysteine-Related Genes Alters the Virulence of Entamoeba histolytica. mSystems 2020; 5:5/6/e01095-20. [PMID: 33361325 PMCID: PMC7762796 DOI: 10.1128/msystems.01095-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Studies on the trophozoite of Entamoeba histolytica suggested this organism could accumulate polyploid cells in its proliferative phase and differentiate its cell cycle from that of other eukaryotes. Therefore, a single-cell sequencing technique was used to study the switching of the RNA transcription profiles of single amoebic trophozoites. Entamoeba histolytica is an intestinal protozoan that causes human amoebic colitis and extraintestinal abscesses. Virulence variation is observed in the pathogenicity of E. histolytica trophozoites, but the detailed mechanism remains unclear. Here, a single trophozoite was cultured alone, and the progeny of the trophozoites of each generation were subjected to single-cell RNA sequencing (scRNA-seq) to study the transcriptional profiles of trophozoites. The scRNA-seq analysis indicated the importance of sulfur metabolism and the proteasome pathway in pathogenicity, whereas the isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis did not identify the bulk trophozoites. The trophozoite improved the synthesis of cysteine under cysteine-deficient conditions but downregulated the expression of the intermediate subunit of the lectin of E. histolytica trophozoites and retained the expression of the heavy subunit of lectin, resulting in decreased amoebic phagocytosis and cytotoxicity. The variation in the transmembrane kinase gene family might be critical in regulating the proteasome pathway. Thus, the scRNA-seq technique provided an improved understanding of the biological characteristics and the mechanism of virulence variation of amoebic trophozoites. IMPORTANCE Studies on the trophozoite of Entamoeba histolytica suggested this organism could accumulate polyploid cells in its proliferative phase and differentiate its cell cycle from that of other eukaryotes. Therefore, a single-cell sequencing technique was used to study the switching of the RNA transcription profiles of single amoebic trophozoites. We separated individual trophozoites from axenic cultured trophozoites, CHO cell-incubated trophozoites, and in vivo trophozoites. We found important changes in the sulfur and cysteine metabolism in pathogenicity. The trophozoites strategically regulated the expression of the cysteine-rich protein-encoding genes under cysteine-deficient conditions, thereby decreasing amoebic phagocytosis and cytotoxicity. The single-cell sequencing technique shows evident advantages in comparison with the isobaric tags for relative and absolute quantitation (iTRAQ) proteomic technology (bulk trophozoite level) and reveals the regulation strategy of trophozoites in the absence of exogenous cysteine. This regulation strategy may be the mechanism of virulence variation of amoebic trophozoites.
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Large-scale Identification and Time-course Quantification of Ubiquitylation Events During Maize Seedling De-etiolation. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 17:603-622. [PMID: 32179194 PMCID: PMC7212306 DOI: 10.1016/j.gpb.2018.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/11/2018] [Accepted: 05/04/2018] [Indexed: 01/02/2023]
Abstract
The ubiquitin system is crucial for the development and fitness of higher plants. De-etiolation, during which green plants initiate photomorphogenesis and establish autotrophy, is a dramatic and complicated process that is tightly regulated by a massive number of ubiquitylation/de-ubiquitylation events. Here we present site-specific quantitative proteomic data for the ubiquitylomes of de-etiolating seedling leaves of Zea mays L. (exposed to light for 1, 6, or 12 h) achieved through immunoprecipitation-based high-resolution mass spectrometry (MS). Through the integrated analysis of multiple ubiquitylomes, we identified and quantified 1926 unique ubiquitylation sites corresponding to 1053 proteins. We analyzed these sites and found five potential ubiquitylation motifs, KA, AXK, KXG, AK, and TK. Time-course studies revealed that the ubiquitylation levels of 214 sites corresponding to 173 proteins were highly correlated across two replicate MS experiments, and significant alterations in the ubiquitylation levels of 78 sites (fold change >1.5) were detected after de-etiolation for 12 h. The majority of the ubiquitylated sites we identified corresponded to substrates involved in protein and DNA metabolism, such as ribosomes and histones. Meanwhile, multiple ubiquitylation sites were detected in proteins whose functions reflect the major physiological changes that occur during plant de-etiolation, such as hormone synthesis/signaling proteins, key C4 photosynthetic enzymes, and light signaling proteins. This study on the ubiquitylome of the maize seedling leaf is the first attempt ever to study the ubiquitylome of a C4 plant and provides the proteomic basis for elucidating the role of ubiquitylation during plant de-etiolation.
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Li Y, Yang B, Tian J, Sun W, Wang G, Qian A, Wang C, Shan X, Kang Y. An iTRAQ-Based Comparative Proteomics Analysis of the Biofilm and Planktonic States of Aeromonas veronii TH0426. Int J Mol Sci 2020; 21:ijms21041450. [PMID: 32093365 PMCID: PMC7073075 DOI: 10.3390/ijms21041450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/15/2020] [Accepted: 02/17/2020] [Indexed: 12/22/2022] Open
Abstract
Aeromonas veronii is a virulent fish pathogen that causes extensive economic losses in the aquaculture industry worldwide. In this study, a virulent strain of A. veronii TH0426 was used to establish an in vitro biofilm model. The results show that the biofilm-forming abilities of A. veronii TH0426 were similar in different media, peaking under conditions of 20 °C and pH 6. Further, isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics methods were used to compare the differential expression of A. veronii between the biofilm and planktonic cells. The results show alterations in 277 proteins, with 130 being upregulated and 147 downregulated. Pathway analysis and GO (Gene Ontology) annotations indicated that these proteins are mainly involved in metabolic pathways and the biosynthesis of secondary metabolites and antibiotics. These proteins are the main factors affecting the adaptability of A. veronii to its external environment. MRM (multiple reaction 27 monitoring) and qPCR (qPCR) were used to verify the differential proteins of the selected A. veronii. This is the first report on the biofilm and planktonic cells of A. veronii, thus contributing to studying the infection and pathogenesis of A. veronii.
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Affiliation(s)
- Ying Li
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Bintong Yang
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
- College of Life Science, Changchun Sci-Tech University, Changchun 130118, China
| | - Jiaxin Tian
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Wuwen Sun
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Guiqin Wang
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Aidong Qian
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Chunfeng Wang
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Xiaofeng Shan
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
- Correspondence: (X.-F.S.); (Y.-H.K.); Tel.: +86-13504404077 (X.S.); +86-0431-84533426 (Y.K.)
| | - Yuanhuan Kang
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
- Correspondence: (X.-F.S.); (Y.-H.K.); Tel.: +86-13504404077 (X.S.); +86-0431-84533426 (Y.K.)
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Kwon OK, Ha YS, Lee JN, Kim S, Lee H, Chun SY, Kwon TG, Lee S. Comparative Proteome Profiling and Mutant Protein Identification in Metastatic Prostate Cancer Cells by Quantitative Mass Spectrometry-based Proteogenomics. Cancer Genomics Proteomics 2019; 16:273-286. [PMID: 31243108 DOI: 10.21873/cgp.20132] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND/AIM Prostate cancer (PCa) is the most frequent cancer found in males worldwide. The aim of this study was to identify new biomarkers using mutated peptides for the prognosis and prediction of advanced PCa, based on proteogenomics. MATERIALS AND METHODS The tryptic peptides were analyzed by tandem mass tag-based quantitative proteomics. Proteogenomics were used to identify mutant peptides as novel biomarkers in advanced PCa. RESULTS Using a human database, increased levels of INTS7 and decreased levels of SH3BGRL were found to be associated with the aggressiveness of PCa. Using proteogenomics and a cancer mutation database, 70 mutant peptides were identified in PCa cell lines. Using parallel reaction monitoring, the expression of seven mutant peptides was found to be altered in tumors, amongst which CAPN2 D22E was the most significantly up-regulated mutant peptide in PCa tissues. CONCLUSION Altered mutant peptides present in PCa tissue could be used as new biomarkers in advanced PCa.
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Affiliation(s)
- Oh Kwang Kwon
- BK21 Plus KNU Multi-Omics-based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Yun-Sok Ha
- Department of Urology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Department of Urology, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Jun Nyung Lee
- Department of Urology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Department of Urology, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Sunjoo Kim
- BK21 Plus Team for Creative Leader Program for Pharmacomics-based Future, Pharmacy and Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Hyesuk Lee
- BK21 Plus Team for Creative Leader Program for Pharmacomics-based Future, Pharmacy and Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Bucheon, Republic of Korea
| | - So Young Chun
- Joint Institute for Regenerative Medicine, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Tae Gyun Kwon
- Department of Urology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea .,Department of Urology, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Sangkyu Lee
- BK21 Plus KNU Multi-Omics-based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
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Mitochondrial Metabolism in Cancer. A Tangled Topic. Which Role for Proteomics? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:1-16. [DOI: 10.1007/978-981-13-8367-0_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Speransky S, Serafini P, Caroli J, Bicciato S, Lippman ME, Bishopric NH. A novel RNA aptamer identifies plasma membrane ATP synthase beta subunit as an early marker and therapeutic target in aggressive cancer. Breast Cancer Res Treat 2019; 176:271-289. [PMID: 31006104 PMCID: PMC6555781 DOI: 10.1007/s10549-019-05174-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 12/22/2022]
Abstract
PURPOSE Primary breast and prostate cancers can be cured, but metastatic disease cannot. Identifying cell factors that predict metastatic potential could guide both prognosis and treatment. METHODS We used Cell-SELEX to screen an RNA aptamer library for differential binding to prostate cancer cell lines with high vs. low metastatic potential. Mass spectroscopy, immunoblot, and immunohistochemistry were used to identify and validate aptamer targets. Aptamer properties were tested in vitro, in xenograft models, and in clinical biopsies. Gene expression datasets were queried for target associations in cancer. RESULTS We identified a novel aptamer (Apt63) that binds to the beta subunit of F1Fo ATP synthase (ATP5B), present on the plasma membrane of certain normal and cancer cells. Apt63 bound to plasma membranes of multiple aggressive breast and prostate cell lines, but not to normal breast and prostate epithelial cells, and weakly or not at all to non-metastasizing cancer cells; binding led to rapid cell death. A single intravenous injection of Apt63 induced rapid, tumor cell-selective binding and cytotoxicity in MDA-MB-231 xenograft tumors, associated with endonuclease G nuclear translocation and DNA fragmentation. Apt63 was not toxic to non-transformed epithelial cells in vitro or adjacent normal tissue in vivo. In breast cancer tissue arrays, plasma membrane staining with Apt63 correlated with tumor stage (p < 0.0001, n = 416) and was independent of other cancer markers. Across multiple datasets, ATP5B expression was significantly increased relative to normal tissue, and negatively correlated with metastasis-free (p = 0.0063, 0.00039, respectively) and overall (p = 0.050, 0.0198) survival. CONCLUSION Ecto-ATP5B binding by Apt63 may disrupt an essential survival mechanism in a subset of tumors with high metastatic potential, and defines a novel category of cancers with potential vulnerability to ATP5B-targeted therapy. Apt63 is a unique tool for elucidating the function of surface ATP synthase, and potentially for predicting and treating metastatic breast and prostate cancer.
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Affiliation(s)
- S Speransky
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, USA
| | - P Serafini
- Department of Microbiology & Immunology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, USA
| | - J Caroli
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - S Bicciato
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - M E Lippman
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, USA
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - N H Bishopric
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, USA.
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
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Sohail W, Majeed F, Afroz A. Differential proteome analysis of diabetes mellitus type 2 and its pathophysiological complications. Diabetes Metab Syndr 2018; 12:1125-1131. [PMID: 29907545 DOI: 10.1016/j.dsx.2018.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 06/05/2018] [Indexed: 01/18/2023]
Abstract
The prevalence of Diabetes Mellitus Type 2 (DM 2) is increasing every passing year due to some global changes in lifestyles of people. The exact underlying mechanisms of the progression of this disease are not yet known. However recent advances in the combined omics more particularly in proteomics and genomics have opened a gateway towards the understanding of predetermined genetic factors, progression, complications and treatment of this disease. Here we shall review the recent advances in proteomics that have led to an early and better diagnostic approaches in controlling DM 2 more importantly the comparison of structural and functional protein biomarkers that are modified in the diseased state. By applying these advanced and promising proteomic strategies with bioinformatics applications and bio-statistical tools the prevalence of DM 2 and its associated disorders i-e nephropathy and retinopathy are expected to be controlled.
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Affiliation(s)
- Waleed Sohail
- Department of Biochemistry and Molecular Biology, University of Gujrat, Pakistan.
| | - Fatimah Majeed
- Department of Biochemistry and Molecular Biology, University of Gujrat, Pakistan
| | - Amber Afroz
- Department of Biochemistry and Molecular Biology, University of Gujrat, Pakistan
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Li Y, Zhu M, Huo Y, Zhang X, Liao M. Anti-fibrosis activity of combination therapy with epigallocatechin gallate, taurine and genistein by regulating glycolysis, gluconeogenesis, and ribosomal and lysosomal signaling pathways in HSC-T6 cells. Exp Ther Med 2018; 16:4329-4338. [PMID: 30542382 PMCID: PMC6257822 DOI: 10.3892/etm.2018.6743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/21/2017] [Indexed: 12/24/2022] Open
Abstract
A previous study by our group indicated that combined treatment with taurine, epigallocatechin gallate (EGCG) and genistein protects against liver fibrosis. The aim of the present study was to elucidate the antifibrotic mechanism of this combination treatment using isobaric tag for relative and absolute quantification (iTRAQ)-based proteomics in an activated rat hepatic stellate cell (HSC) line. In the present study, HSC-T6 cells were incubated with taurine, EGCG and genistein, and cellular proteins were extracted and processed for iTRAQ labeling. Quantification and identification of proteins was performed using two-dimensional liquid chromatography coupled with tandem mass spectrometry. Proteomic analysis indicated that the expression of 166 proteins were significantly altered in response to combination treatment with taurine, EGCG and genistein. A total 76 of these proteins were upregulated and 90 were downregulated. Differentially expressed proteins were grouped according to their association with specific Kyoto Encyclopedia of Genes and Genomes pathways. The results indicated that the differentially expressed proteins hexokinase-2 and lysosome-associated membrane glycoprotein 1 were associated with glycolysis, gluconeogenesis and lysosome signaling pathways. The expression of these proteins was validated using western blot analysis; the expression of hexokinase-2 was significantly decreased and the expression of lysosome-associated membrane glycoprotein 1 was significantly increased in HSC-T6 cells treated with taurine, EGCG and genistein compared with the control, respectively (P<0.05). These results were in accordance with the changes in protein expression identified using the iTRAQ approach. Therefore, the antifibrotic effect of combined therapy with taurine, EGCG and genistein may be associated with the activation of several pathways in HSCs, including glycolysis, gluconeogenesis, and the ribosome and lysosome signaling pathways. The differentially expressed proteins identified in the current study may be useful for treatment of liver fibrosis in the future.
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Affiliation(s)
- Yan Li
- Guangxi University Library, Guangxi University, Nanning, Guangxi 530004, P.R. China
| | - Min Zhu
- Guangxi University Library, Guangxi University, Nanning, Guangxi 530004, P.R. China
| | - Yani Huo
- Medical Scientific Research Centre, Key Laboratory of High-Incidence-Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi 530021, P.R. China
| | - Xuerong Zhang
- Medical Scientific Research Centre, Key Laboratory of High-Incidence-Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi 530021, P.R. China
| | - Ming Liao
- Medical Scientific Research Centre, Key Laboratory of High-Incidence-Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi 530021, P.R. China
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Huang L, Liu W, Jiang Q, Zuo Y, Su Y, Zhao L, Qin Y, Yan Q. Integration of Transcriptomic and Proteomic Approaches Reveals the Temperature-Dependent Virulence of Pseudomonas plecoglossicida. Front Cell Infect Microbiol 2018; 8:207. [PMID: 29977868 PMCID: PMC6021524 DOI: 10.3389/fcimb.2018.00207] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/05/2018] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas plecoglossicida is a facultative pathogen that is associated with diseases of multiple fish, mainly at 15–20°C. Although fish disease caused by P. plecoglossicida has led to significant economic losses, the mechanisms of the temperature-dependent virulence are unclear. Here, we identify potential pathogenicity mechanisms and demonstrate the direct regulation of several virulence factors by temperature with transcriptomic and proteomic analyses, quantitative real-time PCR (qRT-PCR), RNAi, pyoverdine (PVD) quantification, the chrome azurol S (CAS) assay, growth curve measurements, a biofilm assay, and artificial infection. The principal component analysis, the heat map generation and hierarchical clustering, together with the functional annotations of the differentially expressed genes (DEGs) demonstrated that, under different growth temperatures, the animation and focus of P. plecoglossicida are quite different, which may be the key to pathogenicity. Genes involved in PVD synthesis and in the type VI secretion system (T6SS) are specifically upregulated at the virulent temperature of 18°C. Silencing of the PVD-synthesis-related genes reduces the iron acquisition, growth, biofilm formation, distribution in host organs and virulence of the bacteria. Silencing of the T6SS genes also leads to the reduction of biofilm formation, distribution in host organs and virulence. These findings reveal that temperature regulates multiple virulence mechanisms in P. plecoglossicida, especially through iron acquisition and T6SS secretion. Meanwhile, integration of transcriptomic and proteomic data provide us with a new perspective into the pathogenesis of P. plecoglossicida, which would not have been easy to catch at either the protein or mRNA differential analyses alone, thus illustrating the power of multi-omics analyses in microbiology.
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Affiliation(s)
- Lixing Huang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Wenjia Liu
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Qingling Jiang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Yanfei Zuo
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Yongquan Su
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lingmin Zhao
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Yingxue Qin
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Qingpi Yan
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde, China
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12
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Low-dose ionizing radiation exposure represses the cell cycle and protein synthesis pathways in in vitro human primary keratinocytes and U937 cell lines. PLoS One 2018; 13:e0199117. [PMID: 29912936 PMCID: PMC6005503 DOI: 10.1371/journal.pone.0199117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 06/03/2018] [Indexed: 01/21/2023] Open
Abstract
The effects of the high-dose ionizing radiation used in radiotherapy have been thoroughly demonstrated in vitro and in vivo. However, the effects of low-dose ionizing radiation (LDIR) such as computed tomography-guided biopsies and X-ray fluoroscopy on skin cells remain controversial. This study investigated the molecular effects of LDIR on the human primary keratinocytes (HPKs) and U937 cells, monocytes-like cell lines. These cells were exposed to 0.1 Gray (Gy) X-ray as LDIR. The modulation of transcription was assessed using a cDNA array, and the protein expression after LDIR exposure was investigated using isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis at 24 hours. These effects were confirmed by immunoblotting analysis. The direct effects of LDIR on the U937 cells and HPKs and the bystander effects of irradiated HPKs on U937 cells were also investigated. LDIR downregulated c-Myc in both U937 cells and HPKs, and upregulated the p21WAF1/CIP1 protein expression in U937 cells along with the activation of TGFβ and protein phosphatase 2A (PP2A). In HPKs, LDIR downregulated the mTOR signaling with repression of S6 and 4EBP1 activation. Similar changes were observed as bystander effects of LDIR. Our findings suggest that LDIR inhibits protein synthesis and induces the cytokines activation associated with inflammation via direct and bystander effects, which might recapitulate the effects of LDIR in inflammated skin structures.
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13
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Zhang Y, Wang Y, Li S, Zhang X, Li W, Luo S, Sun Z, Nie R. ITRAQ-based quantitative proteomic analysis of processed Euphorbia lathyris L. for reducing the intestinal toxicity. Proteome Sci 2018; 16:8. [PMID: 29692685 PMCID: PMC5905050 DOI: 10.1186/s12953-018-0136-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/26/2018] [Indexed: 11/10/2022] Open
Abstract
Background Euphorbia lathyris L., a Traditional Chinese medicine (TCM), is commonly used for the treatment of hydropsy, ascites, constipation, amenorrhea, and scabies. Semen Euphorbiae Pulveratum, which is another type of Euphorbia lathyris that is commonly used in TCM practice and is obtained by removing the oil from the seed that is called paozhi, has been known to ease diarrhea. Whereas, the mechanisms of reducing intestinal toxicity have not been clearly investigated yet. Methods In this study, the isobaric tags for relative and absolute quantitation (iTRAQ) in combination with the liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic method was applied to investigate the effects of Euphorbia lathyris L. on the protein expression involved in intestinal metabolism, in order to illustrate the potential attenuated mechanism of Euphorbia lathyris L. processing. Differentially expressed proteins (DEPs) in the intestine after treated with Semen Euphorbiae (SE), Semen Euphorbiae Pulveratum (SEP) and Euphorbiae Factor 1 (EFL1) were identified. The bioinformatics analysis including GO analysis, pathway analysis, and network analysis were done to analyze the key metabolic pathways underlying the attenuation mechanism through protein network in diarrhea. Western blot were performed to validate selected protein and the related pathways. Results A number of differentially expressed proteins that may be associated with intestinal inflammation were identified. They mainly constituted by part of the cell. The expression sites of them located within cells and organelles. G protein and Eph/Ephrin signal pathway were controlled jointly by SEP and SE. After processing, the extraction of SEP were mainly reflected in the process of cytoskeleton, glycolysis and gluconeogenesis. Conclusions These findings suggest that SE induced an inflammatory response, and activated the Interleukin signaling pathway, such as the Ang/Tie 2 and JAK2/ STAT signaling pathways, which may eventually contribute to injury result from intestinal inflammatory, while SEP could alleviate this injury by down-regulating STAT1 and activating Ang-4 that might reduce the inflammatory response. Our results demonstrated the importance of Ang-4 and STAT1 expression, which are the target proteins in the attenuated of SE after processing based on proteomic investigation. Thus iTRAQ might be a novel candidate method to study scientific connotation of hypothesis that the attenuated of SE after processing expressed lower toxicity from cellular levels.
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Affiliation(s)
- Yu Zhang
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Yingzi Wang
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Shaojing Li
- 2Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dong cheng District, Dongzhimen Neixiang Street on the 16th, Beijing, 100700 People's Republic of China
| | - Xiuting Zhang
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Wenhua Li
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Shengxiu Luo
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Zhenyang Sun
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Ruijie Nie
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
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Li K, Sun J, Yang J, Roberts SM, Zhang X, Cui X, Wei S, Ma LQ. Molecular Mechanisms of Perfluorooctanoate-Induced Hepatocyte Apoptosis in Mice Using Proteomic Techniques. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11380-11389. [PMID: 28885018 DOI: 10.1021/acs.est.7b02690] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The stability of perfluorooctanoate (PFOA) coupled with its wide use cause serious concerns regarding its potential risk to human health. The molecular mechanisms of PFOA-induced hepatotoxicity relevant to human health was investigated using both in vivo (mouse model) and in vitro (human hepatocyte cells, HL-7702) techniques. Both male and female Balb/c mice were administered PFOA at 0.05, 0.5, or 2.5 mg/kg-d for 28-d, with serum PFOA concentrations after exposure being found at environmentally relevant levels. Liver samples were examined for histology and proteomic change using iTRAQ and Western Blotting, showing dose-dependent hepatocyte apoptosis and peroxisome proliferation. At high doses, genotoxicity resulting from ROS hypergeneration was due to suppression of Complex I subunits in the electron transport chain and activation of PPARα in both genders. However, at 0.05 mg/kg-d, Complex I suppression occurred only in females, making them more sensitive to PFOA-induced apoptosis. In vitro assays using HL-7702 cells confirmed that apoptosis was also induced through a similar mechanism. The dose/gender-dependent toxicity mechanisms help to explain some epidemiological phenomena, i.e., liver cancer is not often associated with PFOA exposure in professional workers. Our results demonstrated that a proteomic approach is a robust tool to explore molecular mechanisms of toxic chemicals at environmentally relevant levels.
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Affiliation(s)
- Kan Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Jie Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Jingping Yang
- School of the Medicine, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Stephen M Roberts
- Center for Environmental and Human Toxicology, University of Florida , Gainesville, Florida 32611, United States
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Xinyi Cui
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Si Wei
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Lena Q Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
- Soil and Water Science Department, University of Florida , Gainesville, Florida 32611, United States
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15
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Yang W, Gao Y, Qian Y, Li J, Hu Q. iTRAQ-based quantitative analysis of alveolar bone resorption in rats with experimental periodontitis. Arch Oral Biol 2017. [DOI: 10.1016/j.archoralbio.2017.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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16
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Qin Y, Wei H, Sun H, Hao P, Wang H, Su J, Yu S. Proteomic Analysis of Differences in Fiber Development between Wild and Cultivated Gossypium hirsutum L. J Proteome Res 2017; 16:2811-2824. [PMID: 28683551 DOI: 10.1021/acs.jproteome.7b00122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Upland cotton (Gossypium hirsutum L.) is one of the world's most important fiber crops, accounting for more than 90% of all cotton production. While their wild progenitors have relatively short and coarse, often tan-colored fibers, modern cotton cultivars possess longer, finer, stronger, and whiter fiber. In this study, the wild and cultivated cottons (YU-3 and TM-1) selected show significant differences on fibers at 10 days postanthesis (DPA), 20 DPA, and mature stages at the morphological level. To explore the effects of domestication, reveal molecular mechanisms underlying these phenotypic differences, and better inform our efforts to further enhance cotton fiber quality, isobaric tags for relative and absolute protein quantification-facilitated proteomic methods were performed on developing fibers. There were 6990 proteins identified; among them, 336 were defined as differentially expressed proteins between fibers of wild versus domesticated cotton. The down- or up-regulated proteins in wild cotton were involved in phenylpropanoid biosynthesis, zeatin biosynthesis, fatty acid elongation, and other processes. Association analysis between transcriptome and proteome showed positive correlations between transcripts and proteins at both 10 DPA and 20 DPA. Differences in proteomics have been verified at the mRNA level by quantitative real-time polymerase chain reaction and have been validated at the physiological and biochemical levels by POD (peroxidase) activity assays and ZA (zeatin) content estimates. This work corroborates the major pathways involved in cotton fiber development and demonstrates that POD activity and zeatin content have a great potential related to fiber elongation and thickening.
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Affiliation(s)
- Yuan Qin
- College of Agronomy, Northwest A&F University , No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , No. 38 Huanghe Road, Anyang, Henan 455000, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , No. 38 Huanghe Road, Anyang, Henan 455000, China
| | - Huiru Sun
- College of Agronomy, Northwest A&F University , No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , No. 38 Huanghe Road, Anyang, Henan 455000, China
| | - Pengbo Hao
- College of Agronomy, Northwest A&F University , No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , No. 38 Huanghe Road, Anyang, Henan 455000, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , No. 38 Huanghe Road, Anyang, Henan 455000, China
| | - Junji Su
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , No. 38 Huanghe Road, Anyang, Henan 455000, China
| | - Shuxun Yu
- College of Agronomy, Northwest A&F University , No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , No. 38 Huanghe Road, Anyang, Henan 455000, China
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17
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Sekihara K, Saitoh K, Han L, Ciurea S, Yamamoto S, Kikkawa M, Kazuno S, Taka H, Kaga N, Arai H, Miida T, Andreeff M, Konopleva M, Tabe Y. Targeting mantle cell lymphoma metabolism and survival through simultaneous blockade of mTOR and nuclear transporter exportin-1. Oncotarget 2017; 8:34552-34564. [PMID: 28388555 PMCID: PMC5470990 DOI: 10.18632/oncotarget.16602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 03/16/2017] [Indexed: 12/11/2022] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive B-cell lymphoma with poor prognosis, characterized by aberrant expression of growth-regulating and oncogenic effectors and requiring novel anticancer strategies. The nuclear transporter exportin-1 (XPO1) is highly expressed in MCL and is associated with its pathogenesis. mTOR signaling, a central regulator of cell metabolism, is frequently activated in MCL and is also an important therapeutic target in this cancer. This study investigated the antitumor effects and molecular/metabolic changes induced by the combination of the small-molecule selective inhibitor XPO1 inhibitor KPT-185 and the dual mTORC1/2 kinase inhibitor AZD-2014 on MCL cells. AZD-2014 enhanced the KPT-185-induced inhibition of cell growth and repression of cell viability. The combination of KPT-185 and AZD-2014 downregulated c-Myc and heat shock factor 1 (HSF1) with its target heat shock protein 70 (HSP70). As a consequence, the combination caused repression of ribosomal biogenesis demonstrated by iTRAQ proteomic analyses. Metabolite assay by CETOF-MS showed that AZD-2014 enhanced the KPT-185-induced repression of MCL cellular energy metabolism through the TCA (Krebs) cycle, and further repressed KPT-185-caused upregulation of glycolysis.Thus the simultaneous inhibition of XPO1 and mTOR signaling is a novel and promising strategy targeting prosurvival metabolism in MCL.
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Affiliation(s)
- Kazumasa Sekihara
- Department of Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Leading Center for the Development and Research of Cancer Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kaori Saitoh
- Department of Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Lina Han
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Stefan Ciurea
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shinichi Yamamoto
- Department of Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Leading Center for the Development and Research of Cancer Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mika Kikkawa
- Laboratory of Proteomics and Biomolecular Science, Research Support Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Saiko Kazuno
- Laboratory of Proteomics and Biomolecular Science, Research Support Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hikari Taka
- Laboratory of Proteomics and Biomolecular Science, Research Support Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Naoko Kaga
- Laboratory of Proteomics and Biomolecular Science, Research Support Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hajime Arai
- Laboratory of Proteomics and Biomolecular Science, Research Support Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Miida
- Department of Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marina Konopleva
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yoko Tabe
- Department of Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Next Genertion Hematology Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
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18
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Torres S, Garcia-Palmero I, Bartolomé RA, Fernandez-Aceñero MJ, Molina E, Calviño E, Segura MF, Casal JI. Combined miRNA profiling and proteomics demonstrates that different miRNAs target a common set of proteins to promote colorectal cancer metastasis. J Pathol 2017; 242:39-51. [PMID: 28054337 DOI: 10.1002/path.4874] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/13/2016] [Accepted: 01/02/2017] [Indexed: 12/13/2022]
Abstract
The process of liver colonization in colorectal cancer remains poorly characterized. Here, we addressed the role of microRNA (miRNA) dysregulation in metastasis. We first compared miRNA expression profiles between colorectal cancer cell lines with different metastatic properties and then identified target proteins of the dysregulated miRNAs to establish their functions and prognostic value. We found that 38 miRNAs were differentially expressed between highly metastatic (KM12SM/SW620) and poorly metastatic (KM12C/SW480) cancer cell lines. After initial validation, we determined that three miRNAs (miR-424-3p, -503, and -1292) were overexpressed in metastatic colorectal cancer cell lines and human samples. Stable transduction of non-metastatic cells with each of the three miRNAs promoted metastatic properties in culture and increased liver colonization in vivo. Moreover, miR-424-3p and miR-1292 were associated with poor prognosis in human patients. A quantitative proteomic analysis of colorectal cancer cells transfected with miR-424-3p, miR-503, or miR-1292 identified alterations in 149, 129, or 121 proteins, respectively, with an extensive overlap of the target proteins of the three miRNAs. Importantly, down-regulation of two of these shared target proteins, CKB and UBA2, increased cell adhesion and proliferation in colorectal cancer cells. The capacity of distinct miRNAs to regulate the same mRNAs boosts the capacity of miRNAs to regulate cancer metastasis and underscores the necessity of targeting multiple miRNAs for effective cancer therapy. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Sofía Torres
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | - Irene Garcia-Palmero
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | - Rubén A Bartolomé
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | | | - Elena Molina
- Surgical Pathology Department, Hospital Clínico, Madrid, Spain
| | - Eva Calviño
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | - Miguel F Segura
- Laboratory of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - J Ignacio Casal
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
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19
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Identification of protein biomarkers and signaling pathways associated with prostate cancer radioresistance using label-free LC-MS/MS proteomic approach. Sci Rep 2017; 7:41834. [PMID: 28225015 PMCID: PMC5320484 DOI: 10.1038/srep41834] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/28/2016] [Indexed: 12/20/2022] Open
Abstract
Identifying biomarkers and signaling pathways are important for the management of prostate cancer (CaP) radioresistance. In this study, we identified differential proteins and signaling pathways from parental CaP cell lines and CaP radioresistant (RR) sublines using a label-free LC-MS/MS proteomics approach. A total of 309 signaling pathway proteins were identified to be significantly altered between CaP and CaP-RR cells (p ≤ 0.05, fold differences >1.5, ≥80% power). Among these proteins, nineteen are common among three paired CaP cell lines and associated with metastasis, progression and radioresistance. The PI3K/Akt, VEGF and glucose metabolism pathways were identified as the main pathways associated with CaP radioresistance. In addition, the identified potential protein markers were further validated in CaP-RR cell lines and subcutaneous (s.c) animal xenografts by western blotting and immunohistochemistry, respectively and protein aldolase A (ALDOA) was selected for a radiosensitivity study. We found the depletion of ALDOA combined with radiotherapy effectively reduced colony formation, induced more apoptosis and increased radiosensitivity in CaP-RR cells. Our findings indicate that CaP radioresistance is caused by multifactorial traits and downregulation of ALDOA increases radiosensitivity in CaP-RR cells, suggesting that controlling these identified proteins or signaling pathways in combination with radiotherapy may hold promise to overcome CaP radioresistance.
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20
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Wei Y, Zeng B, Zhang H, Chen C, Wu Y, Wang N, Wu Y, Shen L. iTRAQ-Based Proteomics Analysis of Serum Proteins in Wistar Rats Treated with Sodium Fluoride: Insight into the Potential Mechanism and Candidate Biomarkers of Fluorosis. Int J Mol Sci 2016; 17:ijms17101644. [PMID: 27690006 PMCID: PMC5085677 DOI: 10.3390/ijms17101644] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/04/2016] [Accepted: 09/16/2016] [Indexed: 01/01/2023] Open
Abstract
Fluorosis induced by exposure to high level fluoride is quite widespread in the world. The manifestations of fluorosis include dental mottling, bone damage, and impaired malfunction of soft tissues. However, the molecular mechanism of fluorosis has not been clarified until now. To explore the underlying mechanisms of fluorosis and screen out serum biomarkers, we carried out a quantitative proteomics study to identify differentially expressed serum proteins in Wistar rats treated with sodium fluoride (NaF) by using a proteomics approach of isobaric tagging for relative and absolute quantitation (iTRAQ). We fed Wistar rats drinking water that had 50, 150, and 250 mg/L of dissolved NaF for 24 weeks. For the experimental duration, each rat was given an examination of the lower incisors to check for the condition of dental fluorosis (DF). By the end of the treatment, fluoride ion concentration in serum and lower incisors were detected. The results showed that NaF treatment can induce rat fluorosis. By iTRAQ analysis, a total of 37 differentially expressed serum proteins were identified between NaF-treated and control rats. These proteins were further analyzed by bioinformatics, out of which two proteins were validated by enzyme-linked immunoadsorbent assays (ELISA). The major proteins were involved in complement and coagulation cascade, inflammatory response, complement activation, defense response, and wound response, suggesting that inflammation and immune reactions may play a key role in fluorosis pathogenesis. These proteins may contribute to the understanding of the mechanism of fluoride toxicity, and may serve as potential biomarkers for fluorosis.
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Affiliation(s)
- Yan Wei
- Department of Environmental Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, China.
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 550025, China.
| | - Beibei Zeng
- Department of Environmental Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, China.
| | - Hua Zhang
- Department of Environmental Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, China.
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 550025, China.
| | - Cheng Chen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Yanli Wu
- Department of Environmental Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, China.
| | - Nanlan Wang
- Department of Environmental Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, China.
| | - Yanqiu Wu
- Department of Environmental Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, China.
| | - Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, China.
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21
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Harada M, Benito J, Yamamoto S, Kaur S, Arslan D, Ramirez S, Jacamo R, Platanias L, Matsushita H, Fujimura T, Kazuno S, Kojima K, Tabe Y, Konopleva M. The novel combination of dual mTOR inhibitor AZD2014 and pan-PIM inhibitor AZD1208 inhibits growth in acute myeloid leukemia via HSF pathway suppression. Oncotarget 2016; 6:37930-47. [PMID: 26473447 PMCID: PMC4741975 DOI: 10.18632/oncotarget.6122] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/26/2015] [Indexed: 11/25/2022] Open
Abstract
Mammalian target of rapamycin (mTOR) signaling is a critical pathway in the biology of acute myeloid leukemia (AML). Proviral integration site for moloney murine leukemia virus (PIM) serine/threonine kinase signaling takes part in various pathways exerting tumorigenic properties. We hypothesized that the combination of a PIM kinase inhibitor with an mTOR inhibitor might have complementary growth-inhibitory effects against AML. The simultaneous inhibition of the PIM kinase by pan-PIM inhibitor AZD1208 and of mTOR by selective mTORC1/2 dual inhibitor AZD2014 exerted anticancer properties in AML cell lines and in cells derived from primary AML samples with or without supportive stromal cell co-culture, leading to suppressed proliferation and increased apoptosis. The combination of AZD1208 and AZD2014 rapidly activated AMPKα, a negative regulator of translation machinery through mTORC1/2 signaling in AML cells; profoundly inhibited AKT and 4EBP1 activation; and suppressed polysome formation. Inhibition of both mTOR and PIM counteracted induction of heat-shock family proteins, uncovering the master negative regulation of heat shock factor 1 (HSF1), the dominant transcription factor controlling cellular stress responses. The novel combination of the dual mTOR inhibitor and pan-PIM inhibitor synergistically inhibited AML growth by effectively reducing protein synthesis through heat shock factor pathway suppression.
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Affiliation(s)
- Masako Harada
- Research Institute for Environmental and Gender Specific Medicine, Juntendo University of Medicine, Tokyo, Japan.,Department of Laboratory Medicine, Juntendo University of Medicine, Tokyo, Japan
| | - Juliana Benito
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shinichi Yamamoto
- Department of Laboratory Medicine, Juntendo University of Medicine, Tokyo, Japan
| | - Surinder Kaur
- Division of Hematology-Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Medical School, Chicago, Illinois, USA
| | - Dirim Arslan
- Division of Hematology-Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Medical School, Chicago, Illinois, USA
| | - Santiago Ramirez
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rodrigo Jacamo
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Leonidas Platanias
- Division of Hematology-Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Medical School, Chicago, Illinois, USA
| | - Hiromichi Matsushita
- Department of Laboratory Medicine, Tokai University School of Medicine, Kanagawa, Japan
| | - Tsutomu Fujimura
- BioMedical Research Center, Juntendo University of Medicine, Tokyo, Japan.,Laboratory of Bioanalytical Chemistry, Tohoku Pharmaceutical University, Miyagi, Japan
| | - Saiko Kazuno
- BioMedical Research Center, Juntendo University of Medicine, Tokyo, Japan
| | - Kensuke Kojima
- Hematology, Respiratory Medicine and Oncology, Department of Medicine, Saga University, Saga, Japan
| | - Yoko Tabe
- Department of Laboratory Medicine, Juntendo University of Medicine, Tokyo, Japan.,Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marina Konopleva
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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22
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Peng F, Huang Y, Li MY, Li GQ, Huang HC, Guan R, Chen ZC, Liang SP, Chen YH. Dissecting characteristics and dynamics of differentially expressed proteins during multistage carcinogenesis of human colorectal cancer. World J Gastroenterol 2016; 22:4515-4528. [PMID: 27182161 PMCID: PMC4858633 DOI: 10.3748/wjg.v22.i18.4515] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/13/2016] [Accepted: 03/18/2016] [Indexed: 02/06/2023] Open
Abstract
AIM: To discover novel biomarkers for early diagnosis, prognosis or treatment of human colorectal cancer.
METHODS: iTRAQ 2D LC-MS/MS analysis was used to identify differentially expressed proteins (DEPs) in the human colonic epithelial carcinogenic process using laser capture microdissection-purified colonic epithelial cells from normal colon, adenoma, carcinoma in situ and invasive carcinoma tissues.
RESULTS: A total of 326 DEPs were identified, and four DEPs (DMBT1, S100A9, Galectin-10, and S100A8) with progressive alteration in the carcinogenic process were further validated by immunohistochemistry. The DEPs were involved in multiple biological processes including cell cycle, cell adhesion, translation, mRNA processing, and protein synthesis. Some of the DEPs involved in cellular process such as “translation” and “mRNA splicing” were progressively up-regulated, while some DEPs involved in other processes such as “metabolism” and “cell response to stress” was progressively down-regulated. Other proteins with up- or down-regulation at certain stages of carcinogenesis may play various roles at different stages of the colorectal carcinogenic process.
CONCLUSION: These findings give insights into our understanding of the mechanisms of colorectal carcinogenesis and provide clues for further investigation of carcinogenesis and identification of biomarkers.
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23
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Hua Y, Wang S, Liu Z, Liu X, Zou L, Gu W, Hou Y, Ma Y, Luo Y, Liu J. iTRAQ-based quantitative proteomic analysis of cultivated Pseudostellaria heterophylla and its wild-type. J Proteomics 2016; 139:13-25. [DOI: 10.1016/j.jprot.2016.02.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/20/2016] [Accepted: 02/23/2016] [Indexed: 01/24/2023]
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24
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Chen C, Zhang LG, Liu J, Han H, Chen N, Yao AL, Kang SS, Gao WX, Shen H, Zhang LJ, Li YP, Cao FH, Li ZG. Bioinformatics analysis of differentially expressed proteins in prostate cancer based on proteomics data. Onco Targets Ther 2016; 9:1545-57. [PMID: 27051295 PMCID: PMC4803245 DOI: 10.2147/ott.s98807] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We mined the literature for proteomics data to examine the occurrence and metastasis of prostate cancer (PCa) through a bioinformatics analysis. We divided the differentially expressed proteins (DEPs) into two groups: the group consisting of PCa and benign tissues (P&b) and the group presenting both high and low PCa metastatic tendencies (H&L). In the P&b group, we found 320 DEPs, 20 of which were reported more than three times, and DES was the most commonly reported. Among these DEPs, the expression levels of FGG, GSN, SERPINC1, TPM1, and TUBB4B have not yet been correlated with PCa. In the H&L group, we identified 353 DEPs, 13 of which were reported more than three times. Among these DEPs, MDH2 and MYH9 have not yet been correlated with PCa metastasis. We further confirmed that DES was differentially expressed between 30 cancer and 30 benign tissues. In addition, DEPs associated with protein transport, regulation of actin cytoskeleton, and the extracellular matrix (ECM)–receptor interaction pathway were prevalent in the H&L group and have not yet been studied in detail in this context. Proteins related to homeostasis, the wound-healing response, focal adhesions, and the complement and coagulation pathways were overrepresented in both groups. Our findings suggest that the repeatedly reported DEPs in the two groups may function as potential biomarkers for detecting PCa and predicting its aggressiveness. Furthermore, the implicated biological processes and signaling pathways may help elucidate the molecular mechanisms of PCa carcinogenesis and metastasis and provide new targets for clinical treatment.
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Affiliation(s)
- Chen Chen
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, People's Republic of China
| | - Li-Guo Zhang
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, People's Republic of China
| | - Jian Liu
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, People's Republic of China
| | - Hui Han
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, People's Republic of China
| | - Ning Chen
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, People's Republic of China
| | - An-Liang Yao
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, People's Republic of China
| | - Shao-San Kang
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, People's Republic of China
| | - Wei-Xing Gao
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, People's Republic of China
| | - Hong Shen
- Department of Modern Technology and Education Center, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Long-Jun Zhang
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, People's Republic of China
| | - Ya-Peng Li
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, People's Republic of China
| | - Feng-Hong Cao
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, People's Republic of China
| | - Zhi-Guo Li
- Department of Medical Research Center, International Science and Technology Cooperation Base of Geriatric Medicine, North China University of Science and Technology, Tangshan, People's Republic of China
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25
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Mukaihara K, Suehara Y, Kohsaka S, Kubota D, Toda-Ishii M, Akaike K, Fujimura T, Kobayashi E, Yao T, Ladanyi M, Kaneko K, Saito T. Expression of F-actin-capping protein subunit beta, CAPZB, is associated with cell growth and motility in epithelioid sarcoma. BMC Cancer 2016; 16:206. [PMID: 26965049 PMCID: PMC4787035 DOI: 10.1186/s12885-016-2235-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 03/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A previous proteomics study demonstrated the overexpression of F-actin capping protein subunit beta (CAPZB) in tissue specimens of epithelioid sarcoma (EpiS). The aim of the present study was to elucidate the function of CAPZB in EpiS. METHODS Cellular functional assays were performed in two EpiS cell lines using CAPZB siRNAs. In addition, comparative protein expression analyses using Isobaric Tags for Relative and Absolute Quantitation (i-TRAQ) method were performed to identify the specific proteins whose expression was dysregulated by CAPZB, and analysed the data with the Ingenuity Pathways Analysis (IPA) system using the obtained protein profiles to clarify the functional pathway networks associated with the oncogenic function of CAPZB in EpiS. Additionally, we performed functional assays of the INI1 protein using INI1-overexpressing EpiS cells. RESULTS All 15 EpiS cases showed an immunohistochemical expression of CAPZB, and two EpiS cell lines exhibited a strong CAPZB expression. Silencing of CAPZB inhibited the growth, invasion and migration of the EpiS cells. Analysis of protein profiles using the IPA system suggested that SWI/SNF chromatin-remodeling complexes including INI1 may function as a possible upstream regulator of CAPZB. Furthermore, silencing of CAPZB resulted in a decreased expression of INI1 proteins in the INI1-positive EpiS cells, whereas the induction of INI1 in the INI1-deficient EpiS cells resulted in an increased CAPZB mRNA expression. CONCLUSIONS CAPZB is involved in tumor progression in cases of EpiS, irrespective of the INI1 expression, and may be a potential therapeutic target. The paradoxical relationship between the tumor suppressor INI1 and the oncoprotein CAPZB in the pathogenesis of EpiS remains to be clarified.
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Affiliation(s)
- Kenta Mukaihara
- Department of Orthopedic Surgery, School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yoshiyuki Suehara
- Department of Orthopedic Surgery, School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Shinji Kohsaka
- Department of Medical Genomics Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Daisuke Kubota
- Department of Orthopedic Surgery, School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Midori Toda-Ishii
- Department of Orthopedic Surgery, School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan.,Department of Human Pathology, School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Keisuke Akaike
- Department of Orthopedic Surgery, School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan.,Department of Human Pathology, School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Tsutomu Fujimura
- Laboratory of Biochemical Analysis, Central Laboratory of Medical Sciences, School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Eisuke Kobayashi
- Division of Musculoskeletal Oncology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takashi Yao
- Department of Human Pathology, School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Kazuo Kaneko
- Department of Orthopedic Surgery, School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
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26
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Chan PPY, Wasinger VC, Leong RW. Current application of proteomics in biomarker discovery for inflammatory bowel disease. World J Gastrointest Pathophysiol 2016; 7:27-37. [PMID: 26909226 PMCID: PMC4753187 DOI: 10.4291/wjgp.v7.i1.27] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/13/2015] [Accepted: 01/04/2016] [Indexed: 02/06/2023] Open
Abstract
Recently, the field of proteomics has rapidly expanded in its application towards clinical research with objectives ranging from elucidating disease pathogenesis to discovering clinical biomarkers. As proteins govern and/or reflect underlying cellular processes, the study of proteomics provides an attractive avenue for research as it allows for the rapid identification of protein profiles in a biological sample. Inflammatory bowel disease (IBD) encompasses several heterogeneous and chronic conditions of the gastrointestinal tract. Proteomic technology provides a powerful means of addressing major challenges in IBD today, especially for identifying biomarkers to improve its diagnosis and management. This review will examine the current state of IBD proteomics research and its use in biomarker research. Furthermore, we also discuss the challenges of translating proteomic research into clinically relevant tools. The potential application of this growing field is enormous and is likely to provide significant insights towards improving our future understanding and management of IBD.
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27
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Mukaihara K, Suehara Y, Kohsaka S, Akaike K, Tanabe Y, Kubota D, Ishii M, Fujimura T, Kazuno S, Okubo T, Takagi T, Yao T, Kaneko K, Saito T. Protein Expression Profiling of Giant Cell Tumors of Bone Treated with Denosumab. PLoS One 2016; 11:e0148401. [PMID: 26863138 PMCID: PMC4749282 DOI: 10.1371/journal.pone.0148401] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/18/2016] [Indexed: 11/30/2022] Open
Abstract
Giant cell tumors of bone (GCTB) are locally aggressive osteolytic bone tumors. Recently, some clinical trials have shown that denosumab is a novel and effective therapeutic option for aggressive and recurrent GCTB. This study was performed to investigate the molecular mechanism underlying the therapeutic effect of denosumab. Comparative proteomic analyses were performed using GCTB samples which were taken before and after denosumab treatment. Each expression profile was analyzed using the software program to further understand the affected biological network. One of identified proteins was further evaluated by gelatin zymography and an immunohistochemical analysis. We identified 13 consistently upregulated proteins and 19 consistently downregulated proteins in the pre- and post-denosumab samples. Using these profiles, the software program identified molecular interactions between the differentially expressed proteins that were indirectly involved in the RANK/RANKL pathway and in several non-canonical subpathways including the Matrix metalloproteinase pathway. The data analysis also suggested that the identified proteins play a critical functional role in the osteolytic process of GCTB. Among the most downregulated proteins, the activity of MMP-9 was significantly decreased in the denosumab-treated samples, although the residual stromal cells were found to express MMP-9 by an immunohistochemical analysis. The expression level of MMP-9 in the primary GCTB samples was not correlated with any clinicopathological factors, including patient outcomes. Although the replacement of tumors by fibro-osseous tissue or the diminishment of osteoclast-like giant cells have been shown as therapeutic effects of denosumab, the residual tumor after denosumab treatment, which is composed of only stromal cells, might be capable of causing bone destruction; thus the therapeutic application of denosumab would be still necessary for these lesions. We believe that the protein expression patterns and the results of the network analysis will provide a better understanding of the effects of denosumab administration in patients with GCTB.
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Affiliation(s)
- Kenta Mukaihara
- Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Yoshiyuki Suehara
- Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
- * E-mail:
| | - Shinji Kohsaka
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Keisuke Akaike
- Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Yu Tanabe
- Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Daisuke Kubota
- Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Midori Ishii
- Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Tsutomu Fujimura
- Laboratory of Biochemical Analysis, Central Laboratory of Medical Sciences, Juntendo University School of Medicine, Tokyo, Japan
| | - Saiko Kazuno
- Laboratory of Biochemical Analysis, Central Laboratory of Medical Sciences, Juntendo University School of Medicine, Tokyo, Japan
| | - Taketo Okubo
- Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Tatsuya Takagi
- Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Takashi Yao
- Department of Human Pathology, Juntendo University School of Medicine, Tokyo, Japan
| | - Kazuo Kaneko
- Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, Juntendo University School of Medicine, Tokyo, Japan
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28
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Tabe Y, Hatanaka Y, Nakashiro M, Sekihara K, Yamamoto S, Matsushita H, Kazuno S, Fujimura T, Ikegami T, Nakanaga K, Matsumoto H, Ueno T, Aoki J, Yokomizo T, Konopleva M, Andreeff M, Miida T, Iwabuchi K, Sasai K. Integrative genomic and proteomic analyses identifies glycerol-3-phosphate acyltransferase as a target of low-dose ionizing radiation in EBV infected-B cells. Int J Radiat Biol 2015; 92:24-34. [DOI: 10.3109/09553002.2015.1106021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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29
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Zhang SF, Zhang Y, Xie ZX, Zhang H, Lin L, Wang DZ. iTRAQ-based quantitative proteomic analysis of a toxigenic dinoflagellate Alexandrium catenella and its non-toxic mutant. Proteomics 2015; 15:4041-50. [PMID: 26417864 DOI: 10.1002/pmic.201500156] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 09/01/2015] [Accepted: 09/22/2015] [Indexed: 11/06/2022]
Abstract
Paralytic shellfish toxins (PSTs) are a group of potent neurotoxic alkaloids produced by cyanobacteria and dinoflagellates. The PST biosynthesis gene cluster and several toxin-related proteins have been unveiled in cyanobacteria, yet little is known about dinoflagellates. Here, we compared the protein profiles of a toxin-producing dinoflagellate Alexandrium catenella (ACHK-T) and its non-toxic mutant (ACHK-NT), and characterized differentially displayed proteins using a combination of the iTRAQ-based proteomic approach and the transcriptomic database. Totally 3488 proteins were identified from A. catenella, and proteins involved in carbohydrate, amino acid and energy metabolism were the most abundant. Among them, 185 proteins were differentially displayed: proteins involved in amino acid biosynthesis, protein and carbohydrate metabolism and bioluminescence were more abundant in ACHK-T, while proteins participating in photosynthesis, fatty acid biosynthesis, and the processes occurring in peroxisome displayed higher abundances in ACHK-NT. Seven toxin-related proteins were identified but they varied insignificantly between the two strains. Different carbon and energy utilization strategies were potentially related to the toxin producing ability, and the regulation mechanism of PST biosynthesis was more complex in dinoflagellates. Our study provides the first comprehensive dataset on the dinoflagellate proteome and lays the groundwork for future proteomic study.
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Affiliation(s)
- Shu-Fei Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
| | - Yong Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
| | - Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
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30
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Tabe Y, Kojima K, Yamamoto S, Sekihara K, Matsushita H, Davis RE, Wang Z, Ma W, Ishizawa J, Kazuno S, Kauffman M, Shacham S, Fujimura T, Ueno T, Miida T, Andreeff M. Ribosomal Biogenesis and Translational Flux Inhibition by the Selective Inhibitor of Nuclear Export (SINE) XPO1 Antagonist KPT-185. PLoS One 2015; 10:e0137210. [PMID: 26340096 PMCID: PMC4560410 DOI: 10.1371/journal.pone.0137210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 08/13/2015] [Indexed: 01/01/2023] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive B-cell lymphoma characterized by the aberrant expression of several growth-regulating, oncogenic effectors. Exportin 1 (XPO1) mediates the nucleocytoplasmic transport of numerous molecules including oncogenic growth-regulating factors, RNAs, and ribosomal subunits. In MCL cells, the small molecule KPT-185 blocks XPO1 function and exerts anti-proliferative effects. In this study, we investigated the molecular mechanisms of this putative anti-tumor effect on MCL cells using cell growth/viability assays, immunoblotting, gene expression analysis, and absolute quantification proteomics. KPT-185 exhibited a p53-independent anti-lymphoma effect on MCL cells, by suppression of oncogenic mediators (e.g., XPO1, cyclin D1, c-Myc, PIM1, and Bcl-2 family members), repression of ribosomal biogenesis, and downregulation of translation/chaperone proteins (e.g., PIM2, EEF1A1, EEF2, and HSP70) that are part of the translational/transcriptional network regulated by heat shock factor 1. These results elucidate a novel mechanism in which ribosomal biogenesis appears to be a key component through which XPO1 contributes to tumor cell survival. Thus, we propose that the blockade of XPO1 could be a promising, novel strategy for the treatment of MCL and other malignancies overexpressing XPO1.
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Affiliation(s)
- Yoko Tabe
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
- Department of Clinical Laboratory Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kensuke Kojima
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
| | - Shinichi Yamamoto
- Department of Clinical Laboratory Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Leading Center for the Development and Research of Cancer Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kazumasa Sekihara
- Department of Clinical Laboratory Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Leading Center for the Development and Research of Cancer Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hiromichi Matsushita
- Department of Laboratory Medicine, Tokai University of Medicine, Kanagawa, Japan
| | - Richard Eric Davis
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
| | - Zhiqiang Wang
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
| | - Wencai Ma
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
| | - Jo Ishizawa
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
| | - Saiko Kazuno
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Michael Kauffman
- Karyopharm Therapeutics Inc., Natick, MA, United States of America
| | - Sharon Shacham
- Karyopharm Therapeutics Inc., Natick, MA, United States of America
| | - Tsutomu Fujimura
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Takashi Ueno
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Takashi Miida
- Department of Clinical Laboratory Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
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31
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Shah P, Wang X, Yang W, Toghi Eshghi S, Sun S, Hoti N, Chen L, Yang S, Pasay J, Rubin A, Zhang H. Integrated Proteomic and Glycoproteomic Analyses of Prostate Cancer Cells Reveal Glycoprotein Alteration in Protein Abundance and Glycosylation. Mol Cell Proteomics 2015; 14:2753-63. [PMID: 26256267 DOI: 10.1074/mcp.m115.047928] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Indexed: 12/31/2022] Open
Abstract
Prostate cancer is the most common cancer among men in the U.S. and worldwide, and androgen-deprivation therapy remains the principal treatment for patients. Although a majority of patients initially respond to androgen-deprivation therapy, most will eventually develop castration resistance. An increased understanding of the mechanisms that underline the pathogenesis of castration resistance is therefore needed to develop novel therapeutics. LNCaP and PC3 prostate cancer cell lines are models for androgen-dependence and androgen-independence, respectively. Herein, we report the comparative analysis of these two prostate cancer cell lines using integrated global proteomics and glycoproteomics. Global proteome profiling of the cell lines using isobaric tags for relative and absolute quantitation (iTRAQ) labeling and two- dimensional (2D) liquid chromatography-tandem MS (LC-MS/MS) led to the quantification of 8063 proteins. To analyze the glycoproteins, glycosite-containing peptides were isolated from the same iTRAQ-labeled peptides from the cell lines using solid phase extraction followed by LC-MS/MS analysis. Among the 1810 unique N-linked glycosite-containing peptides from 653 identified N-glycoproteins, 176 glycoproteins were observed to be different between the two cell lines. A majority of the altered glycoproteins were also observed with changes in their global protein expression levels. However, alterations in 21 differentially expressed glycoproteins showed no change at the protein abundance level, indicating that the glycosylation site occupancy was different between the two cell lines. To determine the glycosylation heterogeneity at specific glycosylation sites, we further identified and quantified 1145 N-linked glycopeptides with attached glycans in the same iTRAQ-labeled samples. These intact glycopeptides contained 67 glycan compositions and showed increased fucosylation in PC3 cells in several of the examined glycosylation sites. The increase in fucosylation could be caused by the detected changes in enzymes belonging to the glycan biosynthesis pathways of protein fucosylation observed in our proteomic analysis. The altered protein fucosylation forms have great potential in aiding our understanding of castration resistance and may lead to the development of novel therapeutic approaches and specific detection strategies for prostate cancer.
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Affiliation(s)
- Punit Shah
- From the ‡Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287
| | - Xiangchun Wang
- From the ‡Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287
| | - Weiming Yang
- From the ‡Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287
| | - Shadi Toghi Eshghi
- From the ‡Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287
| | - Shisheng Sun
- From the ‡Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287
| | - Naseruddin Hoti
- From the ‡Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287
| | - Lijun Chen
- From the ‡Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287
| | - Shuang Yang
- From the ‡Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287
| | - Jered Pasay
- From the ‡Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287
| | - Abby Rubin
- From the ‡Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287
| | - Hui Zhang
- From the ‡Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287
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Liu J, Pang C, Wei H, Song M, Meng Y, Ma J, Fan S, Yu S. iTRAQ-facilitated proteomic profiling of anthers from a photosensitive male sterile mutant and wild-type cotton (Gossypium hirsutum L.). J Proteomics 2015; 126:68-81. [PMID: 26047712 DOI: 10.1016/j.jprot.2015.05.031] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/20/2015] [Accepted: 05/25/2015] [Indexed: 11/28/2022]
Abstract
Male sterility is a common phenomenon in flowering plants, and it has been successfully developed in several crops by taking advantage of heterosis. Cotton (Gossypium hirsutum L.) is an important economic crop, used mainly for the production of textile fiber. Using a space mutation breeding technique, a novel photosensitive genetic male sterile mutant CCRI9106 was isolated from the wild-type upland cotton cultivar CCRI040029. To use CCRI9106 in cotton hybrid breeding, it is of great importance to study the molecular mechanisms of its male sterility. Here, histological and iTRAQ-facilitated proteomic analyses of anthers were performed to explore male sterility mechanisms of the mutant. Scanning and transmission electron microscopy of the anthers showed that the development of pollen wall in CCRI9106 was severely defective with a lack of exine formation. At the protein level, 6121 high-confidence proteins were identified and 325 of them showed differential expression patterns between mutant and wild-type anthers. The proteins up- or down-regulated in MT anthers were mainly involved in exine formation, protein degradation, calcium ion binding,etc. These findings provide valuable information on the proteins involved in anther and pollen development, and contribute to elucidate the mechanism of male sterility in upland cotton.
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Affiliation(s)
- Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan Province, China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan Province, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan Province, China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan Province, China
| | - Yanyan Meng
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South Central University for Nationalities, Wuhan 430064, Hubei Province, China
| | - Jianhui Ma
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan Province, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan Province, China.
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Artemether Exhibits Amoebicidal Activity against Acanthamoeba castellanii through Inhibition of the Serine Biosynthesis Pathway. Antimicrob Agents Chemother 2015; 59:4680-8. [PMID: 26014935 DOI: 10.1128/aac.04758-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 05/18/2015] [Indexed: 11/20/2022] Open
Abstract
Acanthamoeba sp. parasites are the causative agents of Acanthamoeba keratitis, fatal granulomatous amoebic encephalitis, and cutaneous infections. However, there are currently no effective drugs for these organisms. Here, we evaluated the activity of the antimalarial agent artemether against Acanthamoeba castellanii trophozoites and identified potential targets of this agent through a proteomic approach. Artemether exhibited in vitro amoebicidal activity in a time- and dose-dependent manner and induced ultrastructural modification and cell apoptosis. The iTRAQ quantitative proteomic analysis identified 707 proteins that were differentially expressed after artemether treatment. We focused on phosphoglycerate dehydrogenase and phosphoserine aminotransferase in the serine biosynthesis pathway because of their importance to the growth and proliferation of protozoan and cancer cells. The expression of these proteins in Acanthamoeba was validated using quantitative real-time PCR and Western blotting after artemether treatment. The changes in the expression levels of phosphoserine aminotransferase were consistent with those of phosphoglycerate dehydrogenase. Therefore, the downregulation of phosphoserine aminotransferase may be due to the downregulation of phosphoglycerate dehydrogenase. Furthermore, exogenous serine might antagonize the activity of artemether against Acanthamoeba trophozoites. These results indicate that the serine biosynthesis pathway is important to amoeba survival and that targeting these enzymes would improve the treatment of Acanthamoeba infections. Artemether may be used as a phosphoglycerate dehydrogenase inhibitor to control or block Acanthamoeba infections.
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Chahrour O, Cobice D, Malone J. Stable isotope labelling methods in mass spectrometry-based quantitative proteomics. J Pharm Biomed Anal 2015; 113:2-20. [PMID: 25956803 DOI: 10.1016/j.jpba.2015.04.013] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 04/05/2015] [Accepted: 04/08/2015] [Indexed: 02/04/2023]
Abstract
Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons.
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Affiliation(s)
| | - Diego Cobice
- Spectroscopy Group, Analytical Services, Almac, UK
| | - John Malone
- Spectroscopy Group, Analytical Services, Almac, UK
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Abstract
This study was aimed to find new biomarkers for diagnosis and prediction of prognosis of sepsis. Serum samples from nonsurvivor, survivor, and control groups were obtained at 12 h after the induction of sepsis and labeled with isobaric tags (iTRAQ) and then analyzed by two-dimensional liquid chromatography and tandem mass spectrometry. Protein identification and quantification were obtained using mass spectrometry and the ProteinPilot software. Bioinformatics annotation was performed by searching against the PANTHER database. Enzyme-linked immunosorbent assays were used to further confirm the protein identification and differential expression. A logistic regression was then used to screen the index set for diagnosis and prognosis of sepsis. We found that 47 proteins were preferentially elevated in septic rats (both nonsurvivors and survivors) compared with the control rats, and 28 proteins were preferentially elevated in the NS rats as compared with the S group. Several biomarkers, such as multimerin 1, ficolin 1, carboxypeptidase N (CPN2), serine protease 1, and platelet factor 4, were tightly correlated with the diagnosis of sepsis. Logistic regression analyses established multimerin 1, pro-platelet basic protein, fibrinogen-α, and fibrinogen-β for prognosis of sepsis.
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Wang YH, Israelsen WJ, Lee D, Yu VWC, Jeanson NT, Clish CB, Cantley LC, Vander Heiden MG, Scadden DT. Cell-state-specific metabolic dependency in hematopoiesis and leukemogenesis. Cell 2014; 158:1309-1323. [PMID: 25215489 DOI: 10.1016/j.cell.2014.07.048] [Citation(s) in RCA: 264] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 06/09/2014] [Accepted: 07/16/2014] [Indexed: 12/21/2022]
Abstract
The balance between oxidative and nonoxidative glucose metabolism is essential for a number of pathophysiological processes. By deleting enzymes that affect aerobic glycolysis with different potencies, we examine how modulating glucose metabolism specifically affects hematopoietic and leukemic cell populations. We find that a deficiency in the M2 pyruvate kinase isoform (PKM2) reduces the levels of metabolic intermediates important for biosynthesis and impairs progenitor function without perturbing hematopoietic stem cells (HSCs), whereas lactate dehydrogenase A (LDHA) deletion significantly inhibits the function of both HSCs and progenitors during hematopoiesis. In contrast, leukemia initiation by transforming alleles putatively affecting either HSCs or progenitors is inhibited in the absence of either PKM2 or LDHA, indicating that the cell-state-specific responses to metabolic manipulation in hematopoiesis do not apply to the setting of leukemia. This finding suggests that fine-tuning the level of glycolysis may be explored therapeutically for treating leukemia while preserving HSC function.
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Affiliation(s)
- Ying-Hua Wang
- Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - William J Israelsen
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dongjun Lee
- Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vionnie W C Yu
- Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nathaniel T Jeanson
- Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Clary B Clish
- Metabolite Profiling Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lewis C Cantley
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - David T Scadden
- Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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Rauniyar N, Yates JR. Isobaric labeling-based relative quantification in shotgun proteomics. J Proteome Res 2014; 13:5293-309. [PMID: 25337643 PMCID: PMC4261935 DOI: 10.1021/pr500880b] [Citation(s) in RCA: 421] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
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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Sui W, Cui Z, Zhang R, Xue W, Ou M, Zou G, Chen J, Dai Y. Comparative proteomic analysis of renal tissue in IgA nephropathy with iTRAQ quantitative proteomics. Biomed Rep 2014; 2:793-798. [PMID: 25279147 DOI: 10.3892/br.2014.318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/20/2014] [Indexed: 11/06/2022] Open
Abstract
Immunoglobulin (Ig) A nephropathy (IgAN) is the most common form of glomerulonephritis. In clinical practice, it is difficult to monitor the repeating relapse in patients suffering from IgAN, which usually occurs within 10 years of end-stage renal disease. In order to identify and quantify the total protein content in the renal tissue of patients with IgAN, isobaric tags for relative and absolute quantification (iTRAQ) technology was performed. iTRAQ coupled with multiple chromatographic fractionation and tandem mass spectrometry was used to analyze the total protein of normal renal tissue in IgAN and healthy patients. The individual proteins were identified by the Mascot search engine and any that were differentially expressed were monitored. A total of 574 different proteins were identified, and 287 proteins were up- or downregulated by >1 fold alteration in levels. The results showed that iTRAQ-based quantitative proteomic technology for the identification and relative quantitation of the renal tissue proteome is efficiently applicable. The differential expression of the proteome profiles for IgAN patients was determined. Further studies using large cohorts of patient samples with long-term clinical follow-up data should be conducted to evaluate the usefulness of the pathogenesis and novel biomarker candidates of IgAN, which may develop a novel technique for the diagnosis of IgAN.
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Affiliation(s)
- Weiguo Sui
- Nephrology Department of the 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Zhenzhen Cui
- Nephrology Department of the 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China ; The Life Science College, Guangxi Normal University, Guilin, Guangxi 541004, P.R. China
| | - Ruohan Zhang
- Nephrology Department of the 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Wen Xue
- Nephrology Department of the 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Minglin Ou
- Nephrology Department of the 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Guimian Zou
- Nephrology Department of the 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Jiejing Chen
- Nephrology Department of the 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China
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iTRAQ-based quantitative proteomics study on the neuroprotective effects of extract of Acanthopanax senticosus harm on SH-SY5Y cells overexpressing A53T mutant α-synuclein. Neurochem Int 2014; 72:37-47. [DOI: 10.1016/j.neuint.2014.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/04/2014] [Accepted: 04/08/2014] [Indexed: 01/10/2023]
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Chen S, Zhao H, Deng J, Liao P, Xu Z, Cheng Y. Comparative proteomics of glioma stem cells and differentiated tumor cells identifies S100A9 as a potential therapeutic target. J Cell Biochem 2014; 114:2795-808. [PMID: 23836528 DOI: 10.1002/jcb.24626] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 06/27/2013] [Indexed: 12/25/2022]
Abstract
Recent studies have suggested the existence of a small subset of cancer cells called cancer stem cells (CSCs), which possess the ability to initiate malignancies, promote tumor formation, drive metastasis, and evade conventional chemotherapies. Elucidation of the specific signaling pathway and mechanism underlying the action of CSCs might improve the efficacy of cancer treatments. In this study, we analyzed differentially expressed proteins between glioma stem cells and differentiated tumor cells isolated from the human glioma cell line, U251, via iTRAQ-tagging combined with two dimensional liquid chromatography tandem MS analysis to identify proteins correlated with specific features of CSCs. Out of a total data set of 559 identified proteins, 29 proteins were up-regulated in the glioma stem cells when compared with the differentiated cells. Interestingly, The expression level of S100A9 was fivefold higher in glioma stem cells than differentiated cells. Similar results were also observed in glioma stem cells derived from other glioma cells. More importantly, knockdown of S100A9 by RNA interference suppressed the proliferation of glioma stem cell line and decreased the growth of xenograft tumors in vivo. Taken together, these results indicate that the tumorigenesis potential of CSCs arises from highly expressed S100A9.
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Affiliation(s)
- Song Chen
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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Zhang K, Pan X, Zheng J, Xu D, Zhang J, Sun L. Comparative tissue proteomics analysis of thoracic aortic dissection with hypertension using the iTRAQ technique. Eur J Cardiothorac Surg 2014; 47:431-8. [PMID: 24760388 DOI: 10.1093/ejcts/ezu171] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To identify differentially expressed proteins from the aortic tissue of thoracic aortic dissection (TAD) with hypertension and normal aorta and to explore the potential molecular pathogenesis of TAD. METHODS Aortic tissue samples were collected from two groups of age- and gender-matched patients with TAD and normal aorta. These samples were subjected to isobaric tags for relative and absolute quantitation analysis to identify the proteins involved in TAD. Signalling pathways were analysed using the Metacore software, and the identified proteins were validated by western blotting. RESULTS A total of 36 proteins were identified between two groups, with 19 of them being significantly down-regulated and 17 up-regulated in patients with TAD. Proteins including fibrillin-1, emilin-1, decorin, protein DJ-1 and histone H4 were validated by western blotting. The enrichment analysis performed using the Metacore process networks data showed that cell adhesion_cell-matrix interactions, proteolysis_extracellular matrix (ECM) remodelling and inflammation_interleukin 6 (IL-6) signalling were the main protein interaction networks involved in TAD. We further observed indications of increased transforming growth factor-β (TGF-β) signalling and impaired aortic wall remodelling, both of which may be molecular mechanisms for the pathogenesis of TAD. CONCLUSIONS The differentially expressed proteins identified in our study are mainly involved in cell-matrix interaction, ECM remodelling and inflammation. These mechanisms, combined with the TGF-β signalling pathway, may play an important role in the pathogenesis of TAD.
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Affiliation(s)
- Kefeng Zhang
- Department of Cardiovascular Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xudong Pan
- Beijing Aortic Disease Center, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Jun Zheng
- Beijing Aortic Disease Center, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Dong Xu
- Department of Cardiovascular Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jian Zhang
- Department of Cardiovascular Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Lizhong Sun
- Beijing Aortic Disease Center, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
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Larkin SET, Zeidan B, Taylor MG, Bickers B, Al-Ruwaili J, Aukim-Hastie C, Townsend PA. Proteomics in prostate cancer biomarker discovery. Expert Rev Proteomics 2014; 7:93-102. [DOI: 10.1586/epr.09.89] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Kambiranda D, Katam R, Basha SM, Siebert S. iTRAQ-based quantitative proteomics of developing and ripening muscadine grape berry. J Proteome Res 2013; 13:555-69. [PMID: 24251720 DOI: 10.1021/pr400731p] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Grapes are among the widely cultivated fruit crops in the world. Grape berries like other nonclimacteric fruits undergo a complex set of dynamic, physical, physiological, and biochemical changes during ripening. Muscadine grapes are widely cultivated in the southern United States for fresh fruit and wine. To date, changes in the metabolites composition of muscadine grapes have been well documented; however, the molecular changes during berry development and ripening are not fully known. The aim of this study was to investigate changes in the berry proteome during ripening in muscadine grape cv. Noble. Isobaric tags for relative and absolute quantification (iTRAQ) MS/MS was used to detect statistically significant changes in the berry proteome. A total of 674 proteins were detected, and 76 were differentially expressed across four time points in muscadine berry. Proteins obtained were further analyzed to provide information about its potential functions during ripening. Several proteins involved in abiotic and biotic stimuli and sucrose and hexose metabolism were upregulated during berry ripening. Quantitative real-time PCR analysis validated the protein expression results for nine proteins. Identification of vicilin-like antimicrobial peptides indicates additional disease tolerance proteins are present in muscadines for berry protection during ripening. The results provide new information for characterization and understanding muscadine berry proteome and grape ripening.
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Affiliation(s)
- Devaiah Kambiranda
- Plant Biotechnology Laboratory, Center for Viticulture and Small Fruit Research, Florida A&M University , 6505 Mahan Drive, Tallahassee, Florida 32317, United States
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Shi Z, Long W, Zhao C, Guo X, Shen R, Ding H. Comparative proteomics analysis suggests that placental mitochondria are involved in the development of pre-eclampsia. PLoS One 2013; 8:e64351. [PMID: 23671712 PMCID: PMC3650054 DOI: 10.1371/journal.pone.0064351] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/15/2013] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION Pre-eclampsia (PE), a severe pregnancy-specific disease characterized by the new onset of hypertension, proteinuria, edema, and a series of other systematic disorders, is a state of widespread mitochondrial dysfunction of the placenta. METHODS We compared the morphology of mitochondria in pre-eclamptic and normotensive placentae using electron microscopy. To reveal the systematic protein expression changes of placental mitochondria that might explain the pathogenesis of PE, we performed iTRAQ analysis combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) on differentially expressed placental mitochondria proteins from 4 normotensive and 4 pre-eclamptic pregnancies. Bioinformatics analysis was used to find the relative processes that these differentially expressed proteins were involved in. Three differentially expressed proteins were chosen to confirm by Western blotting and immunohistochemistry. RESULTS Morphological data demonstrated degenerative and apoptotic changes in the mitochondria of pre-eclamptic placentae. We found four proteins were upregulated and 22 proteins were downregulated in pre-eclamptic placentae compared with normotensive placentae. Bioinformatics analysis showed that these proteins were involved in many critical processes in the development of pre-eclampsia such as apoptosis, fatty acid oxidation, the respiratory chain, reactive oxygen species generation, the tricarboxylic acid cycle and oxidative stress. CONCLUSIONS This preliminary work provides a better understanding of the proteomic alterations of mitochondria from pre-eclamptic placentae and may aid in our understanding of the importance of mitochondria in the development of pre-eclampsia.
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Affiliation(s)
- Zhonghua Shi
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Wei Long
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Chun Zhao
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Xirong Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Rong Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Hongjuan Ding
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
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Brown NJ, Higham SE, Perunovic B, Arafa M, Balasubramanian S, Rehman I. Lactate dehydrogenase-B is silenced by promoter methylation in a high frequency of human breast cancers. PLoS One 2013; 8:e57697. [PMID: 23437403 PMCID: PMC3578788 DOI: 10.1371/journal.pone.0057697] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 01/28/2013] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE Under normoxia, non-malignant cells rely on oxidative phosphorylation for their ATP production, whereas cancer cells rely on Glycolysis; a phenomenon known as the Warburg effect. We aimed to elucidate the mechanisms contributing to the Warburg effect in human breast cancer. EXPERIMENTAL DESIGN Lactate Dehydrogenase (LDH) isoenzymes were profiled using zymography. LDH-B subunit expression was assessed by reverse transcription PCR in cells, and by Immunohistochemistry in breast tissues. LDH-B promoter methylation was assessed by sequencing bisulfite modified DNA. RESULTS Absent or decreased expression of LDH isoenzymes 1-4, were seen in T-47D and MCF7 cells. Absence of LDH-B mRNA was seen in T-47D cells, and its expression was restored following treatment with the demethylating agent 5'Azacytadine. LDH-B promoter methylation was identified in T-47D and MCF7 cells, and in 25/25 cases of breast cancer tissues, but not in 5/5 cases of normal breast tissues. Absent immuno-expression of LDH-B protein (<10% cells stained), was seen in 23/26 (88%) breast cancer cases, and in 4/8 cases of adjacent ductal carcinoma in situ lesions. Exposure of breast cancer cells to hypoxia (1% O(2)), for 48 hours resulted in significant increases in lactate levels in both MCF7 (14.0 fold, p = 0.002), and T-47D cells (2.9 fold, p = 0.009), but not in MDA-MB-436 (-0.9 fold, p = 0.229), or MCF10AT (1.2 fold, p = 0.09) cells. CONCLUSIONS Loss of LDH-B expression is an early and frequent event in human breast cancer occurring due to promoter methylation, and is likely to contribute to an enhanced glycolysis of cancer cells under hypoxia.
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Affiliation(s)
- Nicola J Brown
- Department of Oncology, The Medical School, University of Sheffield, Sheffield, United Kingdom
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Zeng J, Liu Y, Liu W, Liu X, Liu F, Huang P, Zhu P, Chen J, Shi M, Guo F, Cheng P, Zeng J, Liao Y, Gong J, Zhang HM, Wang D, Guo AY, Xiong X. Integration of transcriptome, proteome and metabolism data reveals the alkaloids biosynthesis in Macleaya cordata and Macleaya microcarpa. PLoS One 2013; 8:e53409. [PMID: 23326424 PMCID: PMC3541140 DOI: 10.1371/journal.pone.0053409] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 11/29/2012] [Indexed: 12/22/2022] Open
Abstract
Background The Macleaya spp., including Macleaya cordata and Macleaya microcarpa, are traditional anti-virus, inflammation eliminating, and insecticide herb medicines for their isoquinoline alkaloids. They are also known as the basis of the popular natural animal food addictive in Europe. However, few studies especially at genomics level were conducted on them. Hence, we performed the Macleaya spp. transcriptome and integrated it with iTRAQ proteome analysis in order to identify potential genes involved in alkaloids biosynthesis. Methodology and Principal Findings We elaborately designed the transcriptome, proteome and metabolism profiling for 10 samples of both species to explore their alkaloids biosynthesis. From the transcriptome data, we obtained 69367 and 78255 unigenes for M. cordata and M. microcarpa, in which about two thirds of them were similar to sequences in public databases. By metabolism profiling, reverse patterns for alkaloids sanguinarine, chelerythrine, protopine, and allocryptopine were observed in different organs of two species. We characterized the expressions of enzymes in alkaloid biosynthesis pathways. We also identified more than 1000 proteins from iTRAQ proteome data. Our results strongly suggest that the root maybe the organ for major alkaloids biosynthesis of Macleaya spp. Except for biosynthesis, the alkaloids storage and transport were also important for their accumulation. The ultrastructure of laticifers by SEM helps us to prove the alkaloids maybe accumulated in the mature roots. Conclusions/Significance To our knowledge this is the first study to elucidate the genetic makeup of Macleaya spp. This work provides clues to the identification of the potential modulate genes involved in alkaloids biosynthesis in Macleaya spp., and sheds light on researches for non-model medicinal plants by integrating different high-throughput technologies.
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Affiliation(s)
- Jianguo Zeng
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
- * E-mail: (JZ); (AG); (XX)
| | - Yisong Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
| | - Wei Liu
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Nextomics Biosciences Co., Ltd. Wuhan, China
| | - Xiubing Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
| | | | - Peng Huang
- Herbal Extract Engineering Research Center (HerbEx), Hunan, China
- Micolta BioResource Inc., Hunan, China
| | - Pengcheng Zhu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
| | - Jinjun Chen
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
| | | | | | - Pi Cheng
- Herbal Extract Engineering Research Center (HerbEx), Hunan, China
| | - Jing Zeng
- Herbal Extract Engineering Research Center (HerbEx), Hunan, China
| | - Yifang Liao
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Nextomics Biosciences Co., Ltd. Wuhan, China
| | - Jing Gong
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Nextomics Biosciences Co., Ltd. Wuhan, China
| | - Hong-Mei Zhang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Nextomics Biosciences Co., Ltd. Wuhan, China
| | - Depeng Wang
- Nextomics Biosciences Co., Ltd. Wuhan, China
| | - An-Yuan Guo
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- * E-mail: (JZ); (AG); (XX)
| | - Xingyao Xiong
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
- * E-mail: (JZ); (AG); (XX)
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Pin E, Fredolini C, Petricoin EF. The role of proteomics in prostate cancer research: biomarker discovery and validation. Clin Biochem 2012; 46:524-38. [PMID: 23266295 DOI: 10.1016/j.clinbiochem.2012.12.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/10/2012] [Accepted: 12/12/2012] [Indexed: 01/06/2023]
Abstract
PURPOSE Prostate Cancer (PCa) represents the second most frequent type of tumor in men worldwide. Incidence increases with patient age and represents the most important risk factor. PCa is mostly characterized by indolence, however in a small percentage of cases (3%) the disease progresses to a metastatic state. To date, the most important issue concerning PCa research is the difficulty in distinguishing indolent from aggressive disease. This problem frequently results in low-grade PCa patient overtreatment and, in parallel; an effective treatment for distant and aggressive disease is not yet available. RESULT Proteomics represents a promising approach for the discovery of new biomarkers able to improve the management of PCa patients. Markers more specific and sensitive than PSA are needed for PCa diagnosis, prognosis and response to treatment. Moreover, proteomics could represent an important tool to identify new molecular targets for PCa tailored therapy. Several possible PCa biomarkers sources, each with advantages and limitations, are under investigation, including tissues, urine, serum, plasma and prostatic fluids. Innovative high-throughput proteomic platforms are now identifying and quantifying new specific and sensitive biomarkers for PCa detection, stratification and treatment. Nevertheless, many putative biomarkers are still far from being applied in clinical practice. CONCLUSIONS This review aims to discuss the recent advances in PCa proteomics, emphasizing biomarker discovery and their application to clinical utility for diagnosis and patient stratification.
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Affiliation(s)
- Elisa Pin
- George Mason University, Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
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O'Connell K, Prencipe M, O'Neill A, Corcoran C, Rani S, Henry M, Dowling P, Meleady P, O'Driscoll L, Watson W, O'Connor R. The use of LC-MS to identify differentially expressed proteins in docetaxel-resistant prostate cancer cell lines. Proteomics 2012; 12:2115-26. [PMID: 22623417 DOI: 10.1002/pmic.201100489] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Docetaxel is a taxane-derived chemotherapy drug that has been approved for treatment of prostate cancer. While docetaxel is frequently used as a treatment for hormone-refractory prostate cancer, a subset of patients either do not respond to this treatment or those that do respond eventually become resistant to the drug over time. Resistance to docetaxel is complex and multi-factoral and further understanding of the cellular biochemistry underlying resistance is vital to improve treatment efficacy. To identify proteins altered in the resistant phenotype, three parental cell lines DU145, 22RV1 and PC-3, as well as their docetaxel resistant sub-lines, were subjected to quantitative label-free LC-MS proteomic profiling. A total of 189 significant (p < 0.05) protein abundance changes were identified in the DU145 resistant sub-lines, 254 in the 22RV1 sub-lines, and 51 and 72 in the 8 and 12 nM resistant PC-3 sub-lines, respectively. From these, 29 proteins demonstrated a significant (p < 0.05) fold change across two or more resistant variants. These included proteins indicative of an epithelial-to-mesenchemyl transition as well as altered heat shock response elements.
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Affiliation(s)
- Kathleen O'Connell
- MTCI, National Institute for Cellular Biotechnology, DCU, Glasnevin, Dublin, Ireland.
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Zhang WW, He X, Lv XP, Li Y, Li HT, Luo R, Li CP, He M. Screening of differentially expressed serum proteins in patients with HBV-related liver fibrosis by iTRAQ combined with mass spectrometry. Shijie Huaren Xiaohua Zazhi 2012; 20:2789-2794. [DOI: 10.11569/wcjd.v20.i29.2789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To screen differentially expressed serum proteins in patients with hepatitis B virus (HBV)-related liver fibrosis using isobaric tags for relative and absolute quantitation (iTRAQ) combined with mass spectrometry.
METHODS: Thirty patients with HBV-related liver fibrosis and 30 healthy volunteers were selected, and their serum samples, after removal of 14 kinds of high-abundant proteins, were used for screening serum differentially expressed serum proteins using iTRAQ labeling and MALDI-TOF-MS. Differentially expressed serum proteins were then analyzed using biological methods.
RESULTS: A total of 274 serum proteins were identified in both healthy volunteers and patients with HBV-related liver fibrosis by mass spectrometry, of which 20 were differentially expressed between the two groups of subjects. Of the 20 differentially expressed serum proteins, 13 were up-regulated and 7 down-regulated. These differentially expressed proteins are involved in 48 biological processes, 8 cellular components, and 12 molecular pathways. APOC3, CLU, C4B, CRP, and APOE were found to be located in the connected nodes of the protein functional interaction network.
CONCLUSION: Serum proteins of APOC3, CLU, C4B, CRP and APOE may play an important role in the development and progression of HBV-related liver fibrosis.
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Peter S, Evans C, Ow SY, Scutt AM, Wright PC, Biggs CA. Proteomic analysis of the impact of static culturing on the expansion of rat bone marrow mesenchymal stem cells. Biotechnol Lett 2012; 34:1589-96. [DOI: 10.1007/s10529-012-0935-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Accepted: 04/17/2012] [Indexed: 10/28/2022]
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