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Pang C, Xu H, Xu J, Zhang L, Wang J, Jing S. Qualifying P-glycoprotein in drug-resistant ovarian cancer cells: a dual-mode aptamer probe approach. Analyst 2024. [PMID: 38916121 DOI: 10.1039/d4an00803k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Drug resistance presents a significant obstacle in treating human ovarian cancer. The development of effective methods for detecting drug-resistant cancer cells is pivotal for tailoring personalized therapies and prognostic assessments. In this investigation, we introduce a dual-mode detection technique employing a fluorogenic aptamer probe for the qualification of P-glycoprotein (P-gp) in drug-resistant ovarian cancer cells. The probe, initially in an "off" state due to the proximity of a quencher to the fluorophore, exhibits increased fluorescence intensity upon binding with the target. The fluorescence enhancement shows a linear correlation with both the concentration of P-gp and the presence of P-gp in drug-resistant ovarian cancer cells. This correlation is quantifiable, with detection limits of 1.56 nM and 110 cells per mL. In an alternate mode, the optimized fluorophores, attached to the aptamer, form larger complexes upon binding to the target protein, which diminishes the rotation speed, thereby augmenting fluorescence polarization. The alteration in fluorescence polarization enables the quantitative analysis of P-gp in the cells, ranging from 100 to 1500 cells per milliliter, with a detection limit of 40 cells per mL. Gene expression analyses, protein expression studies, and immunofluorescence imaging further validated the reliability of our aptamer-based probe for its specificity towards P-gp in drug-resistant cancer cells. Our findings underscore that the dual-mode detection approach promises to enhance the diagnosis and treatment of multidrug-resistant ovarian cancer.
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Affiliation(s)
- Chaobin Pang
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Heng Xu
- Jiangsu Provincial Institute of Materia Medica, Nanjing Tech University, Nanjing, 211816, China
- Nanjing Health Run Biotechnology Co., Ltd, Nanjing, 211316, China
| | - Jichao Xu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Lei Zhang
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Jinhua Wang
- Department of Gynecological Oncology Surgery, Jiangsu Cancer Hospital (Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital), 42 Baiziting Road, Nanjing 210009, Jiangsu Province, China.
- Department of Gynaecology, NO.1 Hospital of Xining, 10 Huzhuxiang Road, Xining 810099, Qinghai Province, China
| | - Su Jing
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
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2
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Zhang Y, Zhu M, Zhu J, Xu F, Chen Y. Nanoproteomics deciphers the prognostic value of EGFR family proteins-based liquid biopsy. Anal Biochem 2023; 671:115133. [PMID: 37011758 DOI: 10.1016/j.ab.2023.115133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/04/2023]
Abstract
Monitoring tumor-associated protein status in serum can effectively track tumors and avoid time-consuming, costly, and invasive tissue biopsy. Epidermal growth factor receptor (EGFR) family proteins are often recommended in the clinical management of multiple solid tumors. However, the low-abundance of serum EGFR (sEGFR) family proteins hinders the depth-understanding of their function and tumor management. Herein, a nanoproteomics approach coupling with aptamer-modified MOFs (NMOFs-Apt) with mass spectrometry was developed for the enrichment and quantitative analysis of sEGFR family proteins. This nanoproteomics approach exhibited high sensitivity and specificity for sEGFR family protein quantification, with the limit of quantification as low as 1.00 nM. After detecting 626 patients' sEGFR family proteins with various malignant tumors, we concluded that the levels of serum proteins had a moderate concordance with tissue counterparts. Metastatic breast cancer patients with a high level of serum human epidermal growth factor receptor 2 (sHER2) and a low level of sEGFR had a poor prognosis, and patients with a sHER2 decrease of more than 20% had longer disease-free time after receiving chemotherapy. This nanoproteomics method provided a simple and effective approach for low-abundant serum protein detection and our results clarified the potential of sHER2 and sEGFR as cancer markers.
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Affiliation(s)
- Yuanyuan Zhang
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Mingchen Zhu
- Department of Clinical Laboratory, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, China
| | - Jianhua Zhu
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Feifei Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China; State Key Laboratory of Reproductive Medicine, 210029, China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Nanjing, 210029, China.
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3
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Adegbola SO, Sarafian M, Sahnan K, Pechlivanis A, Phillips RKS, Warusavitarne J, Faiz O, Haddow J, Knowles C, Tozer P, Holmes E, Hart A. Lack of anti-TNF drugs levels in fistula tissue - a reason for nonresponse in Crohn's perianal fistulating disease? Eur J Gastroenterol Hepatol 2022; 34:18-26. [PMID: 33522723 DOI: 10.1097/meg.0000000000002032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
INTRODUCTION Anti-TNF therapy is recommended as treatment for patients with Crohn´s perianal fistulas. However, a significant proportion of patients have a sub-optimal response to anti-TNF therapy. Higher serum levels of anti-TNF agents have been associated with improved outcomes in perianal Crohn's disease. Currently, it is unknown whether anti-TNF agent levels can be detected in tissue from fistula tracts themselves and whether this is associated with response. AIMS AND METHODS We undertook a pilot study to measure fistula tissue levels of anti-TNF medication (infliximab and adalimumab). We used a previously validated targeted proteomic technique, employing ultraperformance liquid chromatography-mass spectrometry, to detect/quantify anti-TNF drugs. Biopsies were obtained from fistula tracts of patients with Crohn's disease on maintenance treatment; with idiopathic (cryptoglandular) fistula tissues used as negative controls as well as positive controls (by spiking the latter tissues with anti-TNF drugs). RESULTS Tissue was sampled from the fistula tracts of seven patients with Crohn's perianal disease (five patients were on adalimumab and two patients were on infliximab). The anti-TNF drugs, infliximab and adalimumab, were not detected in fistula samples from any of the Crohn's patients despite detection in 'spiked' positive control samples. CONCLUSION Absence of detection of the anti-TNF drugs in fistula tissue raises the question on the role of tissue penetrance of anti-TNF drugs in response to therapy. Further work is required in a larger number of patients to validate the findings observed and investigate if any correlation exists between tissue and serum levels of anti-TNF and clinical outcome. SUMMARY Predicting response in Crohn's fistula patients on biologic therapy is difficult with no reliable biomarkers. This pilot study uses targeted proteomics to investigate the potential role of tissue drug levels in acting as a biomarker of treatment response.
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Affiliation(s)
- Samuel O Adegbola
- Robin Phillips Fistula Research Unit, St Mark's Hospital & Academic Institute, Harrow, Middlesex
- Department of Surgery and Cancer, Imperial College London
| | - Magali Sarafian
- Computational Systems Division, Imperial College London, South Kensington Campus
| | - Kapil Sahnan
- Robin Phillips Fistula Research Unit, St Mark's Hospital & Academic Institute, Harrow, Middlesex
- Department of Surgery and Cancer, Imperial College London
| | | | - Robin K S Phillips
- Robin Phillips Fistula Research Unit, St Mark's Hospital & Academic Institute, Harrow, Middlesex
- Department of Surgery and Cancer, Imperial College London
| | - Janindra Warusavitarne
- Robin Phillips Fistula Research Unit, St Mark's Hospital & Academic Institute, Harrow, Middlesex
- Department of Surgery and Cancer, Imperial College London
| | - Omar Faiz
- Robin Phillips Fistula Research Unit, St Mark's Hospital & Academic Institute, Harrow, Middlesex
- Department of Surgery and Cancer, Imperial College London
| | - James Haddow
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Charles Knowles
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Phil Tozer
- Robin Phillips Fistula Research Unit, St Mark's Hospital & Academic Institute, Harrow, Middlesex
- Department of Surgery and Cancer, Imperial College London
| | - Elaine Holmes
- Computational Systems Division, Imperial College London, South Kensington Campus
| | - Ailsa Hart
- Robin Phillips Fistula Research Unit, St Mark's Hospital & Academic Institute, Harrow, Middlesex
- Department of Surgery and Cancer, Imperial College London
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Wu T, Xi X, Chen Y, Jiang C, Zhang Q, Dai G, Bai Y, Zhang W, Ni T, Zou J, Ju W, Xu M. Absolute protein assay for the simultaneous quantification of two epoxide hydrolases in rats by mass spectrometry-based targeted proteomics. J Sep Sci 2021; 44:2754-2763. [PMID: 34008891 DOI: 10.1002/jssc.202100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/30/2021] [Accepted: 05/16/2021] [Indexed: 11/07/2022]
Abstract
Epoxide hydrolases catalyze the hydrolysis of both exogenous and endogenous epoxides to the corresponding vicinal diols by adding water. Microsomal and soluble epoxide hydrolase are two main mammalian enzymes that have been intensely characterized. The purpose of this investigation was to develop and validate a proteomics assay allowing the simultaneous quantification of microsomal and soluble epoxide hydrolase in rats. Protein quantification was realized through targeted proteomics using liquid chromatography with tandem mass spectrometry for the determination of trypsin-specific surrogate peptides after digestion. Stable isotope-labeled peptides were used as the internal standards. The chromatography of the surrogate peptides was performed on an Agilent SB C18 column (100 mm × 4.6 mm, 1.8 µm) with gradient elution. Acetonitrile containing 0.1% formic acid and 0.1% formic acid aqueous solution were used as mobile phases. A multiple reaction monitoring method in a positive ionization mode was used for the simultaneous detection of the peptides. The method was validated concerning the specificity, linearity, within-day and between-day accuracy and precision, matrix effect, stability, and digestion efficiency. The developed assay was successfully used to quantify the protein levels of microsomal and soluble epoxide hydrolase in rat liver, kidney, and heart S9 samples.
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Affiliation(s)
- Ting Wu
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, P. R. China
| | - Xiaoyun Xi
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, P. R. China
| | - Ying Chen
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, P. R. China
| | - Chao Jiang
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, P. R. China
| | - Qian Zhang
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, P. R. China
| | - Guoliang Dai
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, P. R. China
| | - Yongtao Bai
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, P. R. China
| | - Weidong Zhang
- Department of Pharmacy, Changzhou Hospital of Traditional Chinese Medicine, Changzhou, P. R. China
| | - Ting Ni
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, P. R. China
| | - Jiandong Zou
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, P. R. China
| | - Wenzheng Ju
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, P. R. China
| | - Meijuan Xu
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, P. R. China
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Simultaneous and quantitative monitoring transcription factors in human embryonic stem cell differentiation using mass spectrometry-based targeted proteomics. Anal Bioanal Chem 2021; 413:2081-2089. [PMID: 33655347 DOI: 10.1007/s00216-021-03160-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/15/2020] [Accepted: 01/06/2021] [Indexed: 11/27/2022]
Abstract
Human embryonic stem cells (hESCs) can be self-propagated indefinitely in culture while holding the capacity to generate almost all cell types. Although this powerful differentiation ability of hESCs has become a potential source of cell replacement therapies, application of stem cells in clinical practice relies heavily on the exquisite control of their developmental fate. In general, an essential first step in differentiation is to exit the pluripotent state, which is precariously balanced and depends on a variety of factors, mainly centering on the core transcriptional mechanism. To date, much evidence has indicated that transcription factors such as Sox2, Oct4, and Nanog control the self-renewal and pluripotency of hESCs. Their expression displays a restricted spatial-temporal pattern and their small changes in level can significantly affect directed differentiation and the cell type derived. So far, few assays have been developed to monitor this process. Herein, we provided a mass spectrometry (MS)-based approach for simultaneous and quantitative monitoring of these transcription factors, in an attempt to provide insight into their contributions in hESC differentiation.
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6
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Madda R, Chen CM, Wang JY, Chen CF, Chao KY, Yang YM, Wu HY, Chen WM, Wu PK. Proteomic profiling and identification of significant markers from high-grade osteosarcoma after cryotherapy and irradiation. Sci Rep 2020; 10:2105. [PMID: 32034162 PMCID: PMC7005698 DOI: 10.1038/s41598-019-56024-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023] Open
Abstract
Biological reconstruction of allografts and recycled autografts have been widely implemented in high-grade osteogenic sarcoma. For treating tumor-bearing autografts, extracorporeal irradiation (ECIR) and liquid nitrogen (LN) freezing techniques are being used worldwide as a gold standard treatment procedure. Both the methods aim to eradicate the tumor cells from the local recurrence and restore the limb function. Therefore, it is essential and crucial to find, and compare the alterations at molecular and physiological levels of the treated and untreated OGS recycled autografts to obtain valuable clinical information for better clinical practice. Thus, we aimed to investigate the significantly expressed altered proteins from ECIR-and cryotherapy/freezing- treated OGS (n = 12) were compared to untreated OGS (n = 12) samples using LC-ESI-MS/MS analysis, and the selected proteins from this protein panel were verified using immunoblot analysis. From our comparative proteomic analysis identified a total of 131 differentially expressed proteins (DEPs) from OGS. Among these, 91 proteins were up-regulated (2.5 to 3.5-folds), and 40 proteins were down-regulated (0.2 to 0.5 folds) (p < 0.01 and 0.05). The functional enrichment analysis revealed that the identified DEPs have belonged to more than 10 different protein categories include cytoskeletal, extracellular matrix, immune, enzyme modulators, and cell signaling molecules. Among these, we have confirmed two potential candidates’ expressions levels such as Fibronectin and Protein S100 A4 using western blot analysis. Our proteomic study revealed that LN-freezing and ECIR treatments are effectively eradicating tumor cells, and reducing the higher expressions of DEPs at molecular levels which may help in restoring the limb functions of OGS autografts effectively. To the best of our knowledge, this is the first proteomic study that compared proteomic profiles among freezing, ECIR treated with untreated OGS in recycled autografts. Moreover, the verified proteins could be used as prognostic or diagnostic markers that reveal valuable scientific information which may open various therapeutic avenues in clinical practice to improve patient outcomes.
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Affiliation(s)
- Rashmi Madda
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Research and Development, National Yang-Ming University, Taipei, Taiwan
| | - Chao-Ming Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jir-You Wang
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Cheng-Fong Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Kuang-Yu Chao
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Min Yang
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Hsin-Yi Wu
- Instrumentation center, National Taiwan University, Taipei, Taiwan
| | - Wei-Ming Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Po-Kuei Wu
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan. .,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan. .,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan. .,Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
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7
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Xu Z, Ni R, Chen Y. Targeting breast cancer stem cells by a self-assembled, aptamer-conjugated DNA nanotrain with preloading doxorubicin. Int J Nanomedicine 2019; 14:6831-6842. [PMID: 31695364 PMCID: PMC6717853 DOI: 10.2147/ijn.s200482] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 05/15/2019] [Indexed: 12/30/2022] Open
Abstract
Background Cancer relapse and metastasis is an obstacle to the treatment of breast cancer. Breast cancer stem cells (BCSCs), which can evade the killing effect of traditional chemotherapies, such as doxorubicin (DOX), may contribute to cancer development. Therefore, it is necessary to develop novel drugs that can target and eliminate BCSCs. While multiple strategies have been conceived, they are normally limited by the low drug loading capacity. Purpose An aptamer-conjugated DNA nanotrain TA6NT-AKTin-DOX, which consists of a CD44 aptamer TA6, DNA building blocks M1 and M2 conjugated with an AKT inhibitor peptide AKTin individually and DOX, was designed. Methods This DNA nanotrain was prepared through hybridization chain reactionand this highly ordered DNA duplex has plenty of sites where DOX and AKTin can be intercalated or anchored. By performing on MCF-7 BCSCs and tumors by xenografting BCSCs into nude mice, efficacy of the newly prepared drug was evaluated and compared with that of free DOX and various DNA nanotrains. Results TA6NT-AKTin-DOX showed better efficacy both in vitro and in vivo. To some extent, the enhanced efficacy could be attributed to the targeting effect of TA6 and the high drug loading capacity of the nanotrain (~20 DOX molecules). Besides, a synergistic response was demonstrated by combining DOX with AKTin, probably due to that the anchored AKTin can reverse the drug resistance of BCSCs including apoptosis resistance and ABC transporters overexpression via the AKT signaling pathway. Conclusion The aptamer-conjugated DNA nanotrain TA6NT-AKTin-DOX demonstrated its targeting capability to BCSCs.
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Affiliation(s)
- Zhiyuan Xu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Ronghua Ni
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, People's Republic of China.,State Key Laboratory of Reproductive Medicine, Nanjing 210029, People's Republic of China
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Sum of peak intensities outperforms peak area integration in iTRAQ protein expression measurement by LC-MS/MS using a TripleTOF 5600+ platform. Biosci Rep 2019; 39:BSR20190904. [PMID: 31110078 PMCID: PMC6554230 DOI: 10.1042/bsr20190904] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/08/2019] [Accepted: 05/16/2019] [Indexed: 11/17/2022] Open
Abstract
In the field of quantitative proteomics, the Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) technology has demonstrated efficacy for proteome monitoring despite its lack of a consensus for data handling. In the present study, after peptide and protein identification, we compared the widespread quantitation method based on the calculation of MS/MS reporter ion peaks areas ratios (ProteinPilot) to the alternative method based on the calculation of ratios of the sum of peak intensities (jTRAQx [Quant]) and we processed output data with the in-house Customizable iTRAQ Ratios Calculator (CiR-C) algorithm. Quantitation based on peak area ratios displayed no significant linear correlation with Western blot quantitation. In contrast, quantitation based on the sum of peak intensities displayed a significant linear association with Western blot quantitation (non-zero slope; Pearson correlation coefficient test, r = 0.296, P=0.010**) with an average bias of 0.087 ± 0.500 and 95% Limits of Agreement from −0.893 to 1.068. We proposed the Mascot-jTRAQx-CiR-C strategy as a simple yet powerful data processing adjunct to the iTRAQ technology.
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Abstract
Targeted proteomics detects proteins of interest with high sensitivity, quantitative accuracy, and reproducibility. In a targeted proteomics assay, surrogate peptides are generated by proteolytic digestion of target proteins and selected reaction monitoring (SRM) assays are developed to quantify these peptides using liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this report, we describe the details of quantitative analysis of target protein in cells and tissue samples.
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Affiliation(s)
- Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, China.
| | - Liang Liu
- School of Pharmacy, Nanjing Medical University, Nanjing, China
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10
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Development and application of a UPLC–MS/MS method for P-glycoprotein quantification in human tumor cells. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1084:14-22. [DOI: 10.1016/j.jchromb.2018.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 03/01/2018] [Accepted: 03/06/2018] [Indexed: 01/14/2023]
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Quantitative proteomic analysis of pancreatic cyst fluid proteins associated with malignancy in intraductal papillary mucinous neoplasms. Clin Proteomics 2018; 15:17. [PMID: 29713252 PMCID: PMC5907296 DOI: 10.1186/s12014-018-9193-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
Background
The application of advanced imaging technologies for identifying pancreatic cysts has become widespread. However, accurately differentiating between low-grade dysplasia (LGD), high-grade dysplasia (HGD), and invasive intraductal papillary mucinous neoplasms (IPMNs) remains a diagnostic challenge with current biomarkers, necessitating the development of novel biomarkers that can distinguish IPMN malignancy.
Methods Cyst fluid samples were collected from nine IPMN patients (3 LGD, 3 HGD, and 3 invasive IPMN) during their pancreatectomies. An integrated proteomics approach that combines filter-aided sample preparation, stage tip-based high-pH fractionation, and high-resolution MS was applied to acquire in-depth proteomic data of pancreatic cyst fluid and discover marker candidates for IPMN malignancy. Biological processes of differentially expressed proteins that are related to pancreatic cysts and aggressive malignancy were analyzed using bioinformatics tools such as gene ontology analysis and Ingenuity pathway analysis. In order to confirm the validity of the marker candidates, 19 cyst fluid samples were analyzed by western blot.
Results A dataset of 2992 proteins was constructed from pancreatic cyst fluid samples. A subsequent analysis found 2963 identified proteins in individual samples, 2837 of which were quantifiable. Differentially expressed proteins between histological grades of IPMN were associated with pancreatic diseases and malignancy according to ingenuity pathway analysis. Eighteen biomarker candidates that were differentially expressed across IPMN histological grades were discovered—7 DEPs that were upregulated and 11 that were downregulated in more malignant grades. HOOK1 and PTPN6 were validated by western blot in an independent cohort, the results of which were consistent with our proteomic data. Conclusions This study demonstrates that novel biomarker candidates for IPMN malignancy can be discovered through proteomic analysis of pancreatic cyst fluid. Electronic supplementary material The online version of this article (10.1186/s12014-018-9193-1) contains supplementary material, which is available to authorized users.
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12
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Cao Z, Mou R, Cao Z, Lin X, Ma Y, Zhu Z, Chen M. Quantitation of glutathione S-transferases in rice ( Oryza sativa L.) roots exposed to cadmium by liquid chromatography-tandem mass spectrometry using isotope-labeled wing peptides as an internal standard. PLANT METHODS 2017; 13:64. [PMID: 28785299 PMCID: PMC5543549 DOI: 10.1186/s13007-017-0214-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/27/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Plant glutathione S-transferases (GSTs, EC 2.5.1.18) are multifunctional enzymes involved in heavy metal cellular detoxification by conjugating the tripeptide (g-Glu-Cys-Gly) glutathione to heavy metals. Previous studies demonstrated that individual rice GSTs were differentially induced by heavy metal exposure at the mRNA transcript level. However, little information is available concerning changes in protein concentration of rice GSTs under heavy metal stress. Because the correlation between changes in protein concentration and gene expression under abiotic stress is poor, direct determination of rice GSTs protein concentrations during cadmium (Cd) exposure is a more effective and reliable approach to explore possible mechanisms of rice Cd translocation and accumulation. RESULTS This study established an optimized and advanced liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics assay for quantification of OsGSTF14 and OsGSTU6 proteins in Cd-stressed rice roots. The tryptic signature peptides were chosen as surrogate analytes and winged peptides containing the isotope-labeled signature peptides were used as the internal standards. The signature peptides exhibited good linearity in the range of 0.6-60 and 0.3-30 nM, respectively. The limit of detection and limit of quantification were 4.5 and 14.5 µg/g for OsGSTF14, respectively, and 2.1 and 7.0 µg/g for OsGSTU6. The spiking recoveries rates at low, medium and high levels were in the range of 72.5-93.4%, with intra- and inter-day precisions of 5.5-9.1 and 4.2-10.2%, respectively. CONCLUSIONS The assay successfully quantified the temporal and dose responses of OsGSTF14 and OsGSTU6 proteins in Cd-stressed rice roots, with good accuracy, precision and high-throughput. This assay will have significant application in developing quantification methods of other proteins in Cd-stressed rice, which may provide more insight into the mechanisms of Cd translocation and accumulation in rice.
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Affiliation(s)
- Zhenzhen Cao
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Renxiang Mou
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Zhaoyun Cao
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Xiaoyan Lin
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Youning Ma
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Zhiwei Zhu
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Mingxue Chen
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
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13
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A targeted proteomics approach to the quantitative analysis of ERK/Bcl-2-mediated anti-apoptosis and multi-drug resistance in breast cancer. Anal Bioanal Chem 2016; 408:7491-503. [PMID: 27510278 DOI: 10.1007/s00216-016-9847-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 10/21/2022]
Abstract
Apoptosis suppression caused by overexpression of anti-apoptotic proteins is a central factor to the acquisition of multi-drug resistance (MDR) in breast cancer. As a highly conserved anti-apoptotic protein, Bcl-2 can initiate an anti-apoptosis response via an ERK1/2-mediated pathway. However, the details therein are still far from completely understood and a quantitative description of the associated proteins in the biological context may provide more insights into this process. Following our previous attempts in the quantitative analysis of MDR mechanisms, liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics was continually employed here to describe ERK/Bcl-2-mediated anti-apoptosis. A targeted proteomics assay was developed and validated first for the simultaneous quantification of ERK1/2 and Bcl-2. In particular, ERK isoforms (i.e., ERK1 and ERK2) and their differential phosphorylated forms including isobaric ones were distinguished. Using this assay, differential protein levels and site-specific phosphorylation stoichiometry were observed in parental drug-sensitive MCF-7/WT cancer cells and drug-resistant MCF-7/ADR cancer cells and breast tissue samples from two groups of patients who were either suspected or diagnosed to have drug resistance. In addition, quantitative analysis of the time course of both ERK1/2 and Bcl-2 in doxorubicin (DOX)-treated MCF-7/WT cells confirmed these findings. Overall, we propose that targeted proteomics can be used generally to resolve more complex cellular events.
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14
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Xu F, Yang T, Sheng Y, Zhong T, Yang M, Chen Y. Simultaneous Quantification of Protein Phosphorylation Sites using Liquid Chromatography–Tandem Mass Spectrometry-Based Targeted Proteomics: A Linear Algebra Approach for Isobaric Phosphopeptides. J Proteome Res 2014; 13:5452-60. [DOI: 10.1021/pr500339u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Feifei Xu
- School
of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Ting Yang
- School
of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yuan Sheng
- School
of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Ting Zhong
- School
of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Mi Yang
- Nanjing Gulou Hospital, Nanjing 210008, China
| | - Yun Chen
- School
of Pharmacy, Nanjing Medical University, Nanjing 211166, China
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15
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Yang T, Xu F, Zhao Y, Wang S, Yang M, Chen Y. A liquid chromatography-tandem mass spectrometry-based targeted proteomics approach for the assessment of transferrin receptor levels in breast cancer. Proteomics Clin Appl 2014; 8:773-82. [PMID: 24659461 DOI: 10.1002/prca.201300109] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/21/2014] [Accepted: 03/17/2014] [Indexed: 01/14/2023]
Affiliation(s)
- Ting Yang
- School of Pharmacy; Nanjing Medical University; Nanjing China
| | - Feifei Xu
- School of Pharmacy; Nanjing Medical University; Nanjing China
| | - Yi Zhao
- First Affiliated Hospital of Nanjing Medical University; Nanjing China
| | - Shui Wang
- First Affiliated Hospital of Nanjing Medical University; Nanjing China
| | - Mi Yang
- Nanjing Gulou Hospital; Nanjing China
| | - Yun Chen
- School of Pharmacy; Nanjing Medical University; Nanjing China
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16
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Yang T, Chen F, Xu F, Wang F, Xu Q, Chen Y. A liquid chromatography–tandem mass spectrometry-based targeted proteomics assay for monitoring P-glycoprotein levels in human breast tissue. Clin Chim Acta 2014; 436:283-9. [DOI: 10.1016/j.cca.2014.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/11/2014] [Accepted: 06/16/2014] [Indexed: 01/25/2023]
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17
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Xu F, Yang T, Fang D, Xu Q, Chen Y. An investigation of heat shock protein 27 and P-glycoprotein mediated multi-drug resistance in breast cancer using liquid chromatography-tandem mass spectrometry-based targeted proteomics. J Proteomics 2014; 108:188-97. [PMID: 24882106 DOI: 10.1016/j.jprot.2014.05.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 05/13/2014] [Accepted: 05/21/2014] [Indexed: 12/20/2022]
Abstract
UNLABELLED One missing puzzle piece to study heat shock protein 27 (HSP27) in P-glycoprotein (P-gp) mediated multi-drug resistance (MDR) was the amount of HSP27 and the extent of its phosphorylation in the biological context. Liquid chromatography-tandem mass spectrometry (LC/MS/MS)-based targeted proteomics allows researchers to monitor associated proteins and their modification simultaneously and quantitatively. In this study, a targeted proteomics assay was first developed and validated for the quantification of HSP27 and its phosphorylated forms. Using this assay, the level of HSP27 was determined in non-tumoral cells MCF-10A, parental drug-sensitive cancer cells MCF-7/WT and drug-resistant cancer cells MCF-7/ADR. A decrease of HSP27 expression was observed in P-gp overexpressed MCF-7/ADR cells. A quantitative time-course analysis of both HSP27 and P-gp in doxorubicin (DOX)-treated MCF-7/WT cells also implied that HSP27 may participate in the P-gp modulation. Furthermore, stoichiometry of site-specific HSP27 phosphorylation indicated that DOX treatment rapidly induced the HSP27 phosphorylation at Ser82. Moreover, conventional analytical methods were also performed for a comparison. BIOLOGICAL SIGNIFICANCE LC/MS/MS-based targeted proteomics turns out to be a promising quantification approach for the study of proteins in the preclinical and clinical environment. Unfortunately, rare studies applied this technology to detect multiple associated proteins or protein modification in one experiment. This study demonstrated the potential of LC/MS/MS-based targeted proteomics to understand the cell events in a more accurate context of biological system. By the quantitative time-course analysis of HSP27 and its phosphorylated forms at sites of Ser15 and Ser82, the possible role of HSP27 in P-gp mediated MDR was suggested. Further development of targeted proteomics in future may provide more insight into signal transduction pathways upon perturbation of a protein network or changes to a panel of proposed biomarkers in a given disease state.
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Affiliation(s)
- Feifei Xu
- School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing 211166, China
| | - Ting Yang
- School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing 211166, China
| | - Danjun Fang
- School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing 211166, China
| | - Qingqing Xu
- School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing 211166, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing 211166, China.
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