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Zhang X, Wang Y, Wei ZH, An DY, Pu WR, Liu ZS, Huang YP. Improving the Identification of Lysine-Acetylated Peptides Using a Molecularly Imprinted Monolith Prepared by a Deep Eutectic Solvent Monomer. J Proteome Res 2022; 21:325-338. [PMID: 35050640 DOI: 10.1021/acs.jproteome.1c00553] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
To overcome the identification challenge of low-abundance lysine acetylation (Kac), a novel approach based on a molecularly imprinted polymer (MIP) was developed to improve the extraction capacity of Kac peptides in real samples. Green deep eutectic solvents (DESs) were introduced and used as one of the synergistic functional monomers with zinc acrylate (ZnA). Glycine-glycine-alanine-lysine(ac)-arginine (GGAKacR) was chosen as a template and N,N'-methylenbisacrylamide (MBAA) was used as a cross-linker. The obtained GGAKacR-MIP had excellent selectivity for the template with an imprinting factor (IF) of up to 21.4. The histone digest addition experiment demonstrated that GGAKacR-MIP could successfully extract GGAKacR from a complex sample. Finally, the application to the extraction of Kac peptides from mouse liver protein digestion was studied in detail. The number of Kac peptides and Kac proteins identified was 130 and 110, which were 3.71-fold and 3.93-fold higher than those of the untreated sample. In addition, the number of peptides and proteins identified after treatment increased from 5535 and 1092 to 17 149 and 4037 (3.10-fold and 3.70-fold, respectively). The results showed that the obtained MIP may provide an effective technical tool for the identification of Kac-modification and peptide fractionation, as well as a potential approach for simultaneously identifying post-translational-modified proteomic and proteomic information.
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Affiliation(s)
- Xue Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Yang Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ze-Hui Wei
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Dong-Yu An
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Wan-Rong Pu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Zhao-Sheng Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Yan-Ping Huang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
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Identification of potential urine proteins and microRNA biomarkers for the diagnosis of pulmonary tuberculosis patients. Emerg Microbes Infect 2018; 7:63. [PMID: 29636444 PMCID: PMC5893550 DOI: 10.1038/s41426-018-0066-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 02/23/2018] [Accepted: 03/02/2018] [Indexed: 12/31/2022]
Abstract
This study identified urinary biomarkers for tuberculosis (TB) diagnosis. The urine proteomic profiles of 45 pulmonary tuberculosis patients prior to anti-TB treatment and 45 healthy controls were analyzed and compared using two-dimensional electrophoresis with matrix-assisted laser desorption/ionization time of flight mass spectrometry. Nineteen differentially expressed proteins were identified preliminarily, and western blotting and qRT-PCR were performed to confirm these changes at the translational and transcriptional levels, respectively, using samples from 122 additional pulmonary tuberculosis patients and 73 additional healthy controls. Two proteins, mannose-binding lectin 2 and a 35-kDa fragment of inter-α-trypsin inhibitor H4, exhibited the highest differential expression. We constructed a protein-microRNA interaction network that primarily involved complement and inflammatory responses. Eleven microRNAs from microRNA-target protein interactions were screened and validated using qRT-PCR with some of the above samples, including 97 pulmonary tuberculosis patients and 48 healthy controls. Only miR-625-3p exhibited significant differential expression (p < 0.05). miR-625-3p was increased to a greater extent in samples of smear-positive than smear-negative patients. miR-625-3p was predicted to target mannose-binding lectin 2 protein. A binary logistic regression model based on miR-625-3p, mannose-binding lectin 2, and inter-α-trypsin inhibitor H4 was further established. This three-biomarker combination exhibited better performance for tuberculosis diagnosis than individual biomarkers or any two-biomarker combination and generated a diagnostic sensitivity of 85.87% and a specificity of 87.50%. These novel urine biomarkers may significantly improve tuberculosis diagnosis.
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Lin JJ, Wang RYL, Chen JC, Chiu CC, Liao MH, Wu YJ. Cytotoxicity of 11-epi-Sinulariolide Acetate Isolated from Cultured Soft Corals on HA22T Cells through the Endoplasmic Reticulum Stress Pathway and Mitochondrial Dysfunction. Int J Mol Sci 2016; 17:ijms17111787. [PMID: 27801783 PMCID: PMC5133788 DOI: 10.3390/ijms17111787] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/29/2016] [Accepted: 10/12/2016] [Indexed: 12/17/2022] Open
Abstract
Natural compounds from soft corals have been increasingly used for their antitumor therapeutic properties. This study examined 11-epi-sinulariolide acetate (11-epi-SA), an active compound isolated from the cultured soft coral Sinularia flexibilis, to determine its potential antitumor effect on four hepatocellular carcinoma cell lines. Cell viability was investigated using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, and the results demonstrated that 11-epi-SA treatment showed more cytotoxic effect toward HA22T cells. Protein profiling of the 11-epi-SA-treated HA22T cells revealed substantial protein alterations associated with stress response and protein synthesis and folding, suggesting that the mitochondria and endoplasmic reticulum (ER) play roles in 11-epi-SA-initiated apoptosis. Moreover, 11-epi-SA activated caspase-dependent apoptotic cell death, suggesting that mitochondria-related apoptosis genes were involved in programmed cell death. The unfolded protein response signaling pathway-related proteins were also activated on 11-epi-SA treatment, and these changes were accompanied by the upregulated expression of growth arrest and DNA damage-inducible protein (GADD153) and CCAAT/enhancer binding protein (C/EBP) homologous protein (CHOP), the genes encoding transcription factors associated with growth arrest and apoptosis under prolonged ER stress. Two inhibitors, namely salubrinal (Sal) and SP600125, partially abrogated 11-epi-SA-related cell death, implying that the protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK)–activating transcription factor (ATF) 6–CHOP or the inositol-requiring enzyme 1 alpha (IRE1α)–c-Jun N-terminal kinase (JNK)–cJun signal pathway was activated after 11-epi-SA treatment. In general, these results suggest that 11-epi-SA exerts cytotoxic effects on HA22T cells through mitochondrial dysfunction and ER stress cell death pathways.
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Affiliation(s)
- Jen-Jie Lin
- Graduate Institute of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan.
| | - Robert Y L Wang
- Department of Biomedical Sciences and Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan.
- Division of Pediatric Infectious Disease, Department of Pediatrics, Chang Gung Memorial Hospital, Linkuo 33305, Taiwan.
| | - Jiing-Chuan Chen
- Department of Food Science and Nutrition, Meiho University, Pingtung 91202, Taiwan.
| | - Chien-Chih Chiu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
| | - Ming-Hui Liao
- Graduate Institute of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan.
| | - Yu-Jen Wu
- Department of Food Science and Nutrition, Meiho University, Pingtung 91202, Taiwan.
- Department of Beauty Science, Meiho University, Pingtung 91202, Taiwan.
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Human Urine Proteomics: Analytical Techniques and Clinical Applications in Renal Diseases. INTERNATIONAL JOURNAL OF PROTEOMICS 2015; 2015:782798. [PMID: 26693351 PMCID: PMC4677025 DOI: 10.1155/2015/782798] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/09/2015] [Indexed: 12/14/2022]
Abstract
Urine has been in the center of attention among scientists of clinical proteomics in the past decade, because it is valuable source of proteins and peptides with a relative stable composition and easy to collect in large and repeated quantities with a noninvasive procedure. In this review, we discuss technical aspects of urinary proteomics in detail, including sample preparation, proteomic technologies, and their advantage and disadvantages. Several recent experiments are presented which applied urinary proteome for biomarker discovery in renal diseases including diabetic nephropathy, immunoglobulin A (IgA) nephropathy, focal segmental glomerulosclerosis, lupus nephritis, membranous nephropathy, and acute kidney injury. In addition, several available databases in urinary proteomics are also briefly introduced.
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Olszowy P, Buszewski B. Urine sample preparation for proteomic analysis. J Sep Sci 2014; 37:2920-8. [PMID: 25132110 DOI: 10.1002/jssc.201400331] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 07/08/2014] [Accepted: 07/18/2014] [Indexed: 12/22/2022]
Abstract
Sample preparation for both environmental and more importantly biological matrices is a bottleneck of all kinds of analytical processes. In the case of proteomic analysis this element is even more important due to the amount of cross-reactions that should be taken into consideration. The incorporation of new post-translational modifications, protein hydrolysis, or even its degradation is possible as side effects of proteins sample processing. If protocols are evaluated appropriately, then identification of such proteins does not bring difficulties. However, if structural changes are provided without sufficient attention then protein sequence coverage will be reduced or even identification of such proteins could be impossible. This review summarizes obstacles and achievements in protein sample preparation of urine for proteome analysis using different tools for mass spectrometry analysis. The main aim is to present comprehensively the idea of urine application as a valuable matrix. This article is dedicated to sample preparation and application of urine mainly in novel cancer biomarkers discovery.
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Affiliation(s)
- Pawel Olszowy
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Torun, Poland; Interdisciplinary Centre for Modern Technologies, Nicolaus Copernicus University, Torun, Poland
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Lu CM, Lin JJ, Huang HH, Ko YC, Hsu JL, Chen JC, Din ZH, Wu YJ. A panel of tumor markers, calreticulin, annexin A2, and annexin A3 in upper tract urothelial carcinoma identified by proteomic and immunological analysis. BMC Cancer 2014; 14:363. [PMID: 24884814 PMCID: PMC4039341 DOI: 10.1186/1471-2407-14-363] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/20/2014] [Indexed: 12/25/2022] Open
Abstract
Background Upper tract urothelial carcinoma (UTUC) is a tumor with sizable metastases and local recurrence. It has a worse prognosis than bladder cancer. This study was designed to investigate the urinary potential tumor markers of UTUC. Methods Between January 2008 and January 2009, urine was sampled from 13 patients with UTUC and 20 healthy adults. The current study identified biomarkers for UTUC using non-fixed volume stepwise weak anion exchange chromatography for fractionation of urine protein prior to two-dimensional gel electrophoresis. Results Fifty five differential proteins have been determined by comparing with the 2-DE maps of the urine of UTUC patients and those of healthy people. Western blotting analysis and immunohistochemistry of tumor tissues and normal tissues from patients with UTUC were carried out to further verify five possible UTUC biomarkers, including zinc-alpha-2-glycoprotein, calreticulin, annexin A2, annexin A3 and haptoglobin. The data of western blot and immunohistochemical analysis are consistent with the 2-DE data. Combined the experimental data in the urine and in tumor tissues collected from patients with UTUC, the crucial over-expressed proteins are calreticulin, annexin A2, and annexin A3. Conclusions Calreticulin, annexin A2, and annexin A3 are very likely a panel of biomarkers with potential value for UTUC diagnosis.
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Affiliation(s)
| | | | | | | | | | | | | | - Yu-Jen Wu
- Department of Beauty Science, Meiho University, Pingtung, Taiwan.
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Li HH, Su JH, Chiu CC, Lin JJ, Yang ZY, Hwang WI, Chen YK, Lo YH, Wu YJ. Proteomic investigation of the sinulariolide-treated melanoma cells A375: effects on the cell apoptosis through mitochondrial-related pathway and activation of caspase cascade. Mar Drugs 2013; 11:2625-42. [PMID: 23880933 PMCID: PMC3736442 DOI: 10.3390/md11072625] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 07/09/2013] [Accepted: 07/10/2013] [Indexed: 12/22/2022] Open
Abstract
Sinulariolide is an active compound isolated from the cultured soft coral Sinularia flexibilis. In this study, we investigated the effects of sinulariolide on A375 melanoma cell growth and protein expression. Sinulariolide suppressed the proliferation and migration of melanoma cells in a concentration-dependent manner and was found to induce both early and late apoptosis by flow cytometric analysis. Comparative proteomic analysis was conducted to investigate the effects of sinulariolide at the molecular level by comparison between the protein profiles of melanoma cells treated with sinulariolide and those without treatment. Two-dimensional gel electrophoresis (2-DE) master maps of control and treated A375 cells were generated by analysis with PDQuest software. Comparison between these maps showed up- and downregulation of 21 proteins, seven of which were upregulated and 14 were downregulated. The proteomics studies described here identify some proteins that are involved in mitochondrial dysfunction and apoptosis-associated proteins, including heat shock protein 60, heat shock protein beta-1, ubiquinol cytochrome c reductase complex core protein 1, isocitrate dehydrogenase (NAD) subunit alpha (down-regulated), and prohibitin (up-regulated), in A375 melanoma cells exposed to sinulariolide. Sinulariolide-induced apoptosis is relevant to mitochondrial-mediated apoptosis via caspase-dependent pathways, elucidated by the loss of mitochondrial membrane potential, release of cytochrome c, and activation of Bax, Bad and caspase-3/-9, as well as suppression of p-Bad, Bcl-xL and Bcl-2. Taken together, our results show that sinulariolide-induced apoptosis might be related to activation of the caspase cascade and mitochondria dysfunction pathways. Our results suggest that sinulariolide merits further evaluation as a chemotherapeutic agent for human melanoma.
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Affiliation(s)
- Hsing-Hui Li
- National Museum of Marine Biology and Aquarium, Pingtung 94450, Taiwan; E-Mails: (H.-H.L.); (J.-H.S.)
| | - Jui-Hsin Su
- National Museum of Marine Biology and Aquarium, Pingtung 94450, Taiwan; E-Mails: (H.-H.L.); (J.-H.S.)
| | - Chien-Chih Chiu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 80761, Taiwan; E-Mail:
| | - Jen-Jie Lin
- Graduate Institute of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91202, Taiwan; E-Mail:
| | - Zih-Yan Yang
- Graduate Institute of Food Science, National Pingtung University of Science and Technology, Pingtung 91202, Taiwan; E-Mail:
| | - Wen-Ing Hwang
- Department of Food Science and Nutrition, Meiho University, Pingtung 91202, Taiwan; E-Mails: (W.-I.H.); (Y.-K.C.)
| | - Yu-Kuei Chen
- Department of Food Science and Nutrition, Meiho University, Pingtung 91202, Taiwan; E-Mails: (W.-I.H.); (Y.-K.C.)
| | - Yu-Hsuan Lo
- Excellence Biotech Co., Kaohsiung 80655, Taiwan; E-Mail:
| | - Yu-Jen Wu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 80761, Taiwan; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +886-8-7799821 (ext. 8613); Fax: +886-8-7797821
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Su CC, Su JH, Lin JJ, Chen CC, Hwang WI, Huang HH, Wu YJ. An investigation into the cytotoxic effects of 13-acetoxysarcocrassolide from the soft coral Sarcophyton crassocaule on bladder cancer cells. Mar Drugs 2011; 9:2622-2642. [PMID: 22363243 PMCID: PMC3280580 DOI: 10.3390/md9122622] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 11/18/2011] [Accepted: 11/30/2011] [Indexed: 01/01/2023] Open
Abstract
Active compounds from natural products have been widely studied. The anti-tumor effects of 13-acetoxysarcocrassolide isolated from Formosan soft coral Sarcophyton crassocaule on bladder cancer cells were examined in this study. An MTT assay showed that 13-acetoxysarcocrassolide was cytotoxic to bladder female transitional cancer (BFTC) cells. We determined that the BFTC cells underwent cell death through apoptosis by flow cytometry. Due to the highly-migratory nature of the BFTC cells, the ability of 13-acetoxysarcocrassolide to stop their migration was assessed by a wound healing assay. To determine which proteins were affected in the BFTC cells upon treatment, a comparative proteomic analysis was performed. By LC-MS/MS analysis, we identified that 19 proteins were up-regulated and eight were down-regulated. Seven of the proteins were confirmed by western blotting analysis. This study reveals clues to the potential mechanism of the cytotoxic effects of 13-acetoxysarcocrassolide on BFTC cells. Moreover, it suggests that PPT1 and hnRNP F could be new biomarkers for bladder cancer. The results of this study are also helpful for the diagnosis, progression monitoring and therapeutic strategies of transitional cell tumors.
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Affiliation(s)
- Ching-Chyuan Su
- Antai Medical Care Cooperation Antai Tian-Sheng Memorial Hospital, Pingtung 92842, Taiwan;
| | - Jui-Hsin Su
- National Museum of Marine Biology and Aquarium, Pingtung 94446, Taiwan;
| | - Jen-Jie Lin
- Department of Beauty Science, Meiho University, Pingtung 91202, Taiwan; (J.-J.L.); (C.-C.C.)
| | - Cheng-Chi Chen
- Department of Beauty Science, Meiho University, Pingtung 91202, Taiwan; (J.-J.L.); (C.-C.C.)
| | - Wen-Ing Hwang
- Department of Food Science and Nutrition, Meiho University, Pingtung 91202, Taiwan;
| | - Han Hsiang Huang
- Department of Beauty Science, Meiho University, Pingtung 91202, Taiwan; (J.-J.L.); (C.-C.C.)
- Authors to whom correspondence should be addressed; or (Y.-J.W.); (H.H.H.); Tel.: +886-8-7799821 (ext. 8600) (Y.-J.W.); +886-8-7799821 (ext. 8647) (H.H.H.); Fax: +886-8-7793281 (H.H.H.)
| | - Yu-Jen Wu
- Department of Beauty Science, Meiho University, Pingtung 91202, Taiwan; (J.-J.L.); (C.-C.C.)
- Authors to whom correspondence should be addressed; or (Y.-J.W.); (H.H.H.); Tel.: +886-8-7799821 (ext. 8600) (Y.-J.W.); +886-8-7799821 (ext. 8647) (H.H.H.); Fax: +886-8-7793281 (H.H.H.)
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