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Gautam SS, Singh SP. Immunopurification Reagents and Their Application in Biologics and Biomarker Quantitation Using LC-MS/MS in Drug Discovery. J Chromatogr Sci 2023; 61:799-805. [PMID: 36469494 DOI: 10.1093/chromsci/bmac096] [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: 01/26/2022] [Indexed: 10/01/2023]
Abstract
The LC-MS/MS technology is one of the most utilized bio-analytical tools owing to its advantage of selectivity, sensitivity and multitasking. The advent of novel biological therapies and increasing demand for protein biomarker identification and quantitation have put the LC-MS/MS technology at the forefront. The questions which are been posed to the LC-MS/MS scientist are complex. The complexity of the question increases further with the matrices in which these questions need to be answered. To bring down the complexity of the analysis, LC-MS/MS technology is utilizing the immunopurification (IP) technique as the new sample preparation technique. The IP reagents are the most common reagents which are used to decrease the matrices' complexity and allow the LC-MS/MS system to reach greater sensitivity. The utilization of these reagents is increasing every day, but the proper utilization of these reagents is still unknown to the common analyst in drug discovery. The present review throws light on the utilization aspect of these reagents, as we have classified these reagents on basis of their utilization, which will allow the readers to gain an understanding of these reagents. This review will also talk about the merits and the demerits of each approach and the current understanding of utilizing these reagents.
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Affiliation(s)
- Shashyendra Singh Gautam
- Toxicokinetics Laboratory/Analytical Chemistry Laboratory, Regulatory Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 200102, India
- Biocon-Bristol-Myers Squibb Research Centre, Syngene International Ltd, Bangalore 560100, India
| | - Sheelendra Pratap Singh
- Toxicokinetics Laboratory/Analytical Chemistry Laboratory, Regulatory Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 200102, India
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Khuong HL, Chen CH, Lin JL, Le TN, Pham TH, Le TBT, Nguyen XC, Phan VC, Chu HH, Hsiao WWW, Nguyen TMP, Pham DM. Nanodiamond Solid-Phase Extraction and Triton X-114 Cloud Point Separation for Robust Fractionation and Shotgun Proteomics Analysis of the Human Serum Proteome. J Proteome Res 2021; 21:67-76. [PMID: 34928606 DOI: 10.1021/acs.jproteome.1c00510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Human serum is one of the most attractive specimens in biomarker research. However, its overcomplicated properties have hindered the analysis of low-abundance proteins by conventional mass spectrometry techniques. This work proposes an innovative strategy for utilizing nanodiamonds (NDs) in combination with Triton X-114 protein extraction to fractionate the crude serum to six pH-tuned fractions, simplifying the overall proteome and facilitating protein profiling with high efficiency. A total of 663 proteins are identified and evenly distributed among the fractions along with 39 FDA-approved biomarkers─a remarkable increase from the 230 proteins found in unfractionated crude serum. In the low-abundance protein section, 88 proteins with 7 FDA-approved biomarkers are detected─a marked increase from the 15 proteins (2 biomarkers) observed in the untreated sample. Notably, fractions at pH 11, derived from the aqueous phase of detergent separation, suggest potential applications in rapid and robust serum proteome analysis. Notably, by outlining the excellent properties of NDs for proteomic research, this work suggests a promising extraction protocol utilizing the great compatibility of NDs with streamlined serum proteomics and identifies potential avenues for future developments. Finally, we believe that this work not just improves shotgun proteomics but also opens up studies on the interaction between NDs and the human proteome. Data are available via ProteomeXchange with the identifier PXD029710.
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Affiliation(s)
- Hai Lam Khuong
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Chein-Hung Chen
- Genomic Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Jung-Lee Lin
- Genomic Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Trong-Nghia Le
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan
| | - Thi Hue Pham
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Thi Bich Thao Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Xuan Canh Nguyen
- Faculty of Biotechnology, Vietnam National University of Agriculture, Gia Lam, Hanoi 100000, Vietnam
| | - Van Chi Phan
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Hoang Ha Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Wesley Wei-Wen Hsiao
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan
| | - Thi Minh Phuong Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Dinh Minh Pham
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
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Radko S, Ptitsyn K, Novikova S, Kiseleva Y, Moysa A, Kurbatov L, Mannanova M, Zgoda V, Ponomarenko E, Lisitsa A, Archakov A. Evaluation of Aptamers as Affinity Reagents for an Enhancement of SRM-Based Detection of Low-Abundance Proteins in Blood Plasma. Biomedicines 2020; 8:E133. [PMID: 32456365 PMCID: PMC7277749 DOI: 10.3390/biomedicines8050133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Selected reaction monitoring (SRM) is a mass spectrometric technique characterized by the exceptionally high selectivity and sensitivity of protein detection. However, even with this technique, the quantitative detection of low- and ultralow-abundance proteins in blood plasma, which is of great importance for the search and verification of novel protein disease markers, is a challenging task due to the immense dynamic range of protein abundance levels. One approach used to overcome this problem is the immunoaffinity enrichment of target proteins for SRM analysis, employing monoclonal antibodies. Aptamers appear as a promising alternative to antibodies for affinity enrichment. Here, using recombinant protein SMAD4 as a model target added at known concentrations to human blood plasma and SRM as a detection method, we investigated a relationship between the initial amount of the target protein and its amount in the fraction enriched with SMAD4 by an anti-SMAD4 DNA-aptamer immobilized on magnetic beads. It was found that the aptamer-based enrichment provided a 30-fold increase in the sensitivity of SRM detection of SMAD4. These results indicate that the aptamer-based affinity enrichment of target proteins can be successfully employed to improve quantitative detection of low-abundance proteins by SRM in undepleted human blood plasma.
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Affiliation(s)
- Sergey Radko
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Konstantin Ptitsyn
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Svetlana Novikova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Yana Kiseleva
- Russian Scientific Center of Roentgenoradiology, Moscow 117485, Russia;
| | - Alexander Moysa
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Leonid Kurbatov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Maria Mannanova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Victor Zgoda
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Elena Ponomarenko
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Andrey Lisitsa
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Alexander Archakov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
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Nitika, Truman AW. Endogenous epitope tagging of heat shock protein 70 isoform Hsc70 using CRISPR/Cas9. Cell Stress Chaperones 2018; 23:347-355. [PMID: 28944418 PMCID: PMC5904078 DOI: 10.1007/s12192-017-0845-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/13/2017] [Accepted: 09/16/2017] [Indexed: 12/31/2022] Open
Abstract
Heat shock protein 70 (Hsp70) is an evolutionarily well-conserved molecular chaperone involved in several cellular processes such as folding of proteins, modulating protein-protein interactions, and transport of proteins across the membrane. Binding partners of Hsp70 (known as "clients") are identified on an individual basis as researchers discover their particular protein of interest binds to Hsp70. A full complement of Hsp70 interactors under multiple stress conditions remains to be determined. A promising approach to characterizing the Hsp70 "interactome" is the use of protein epitope tagging and then affinity purification followed by mass spectrometry (AP-MS/MS). AP-MS analysis is a widely used method to decipher protein-protein interaction networks and identifying protein functions. Conventionally, the proteins are overexpressed ectopically which interferes with protein complex stoichiometry, skewing AP-MS/MS data. In an attempt to solve this issue, we used CRISPR/Cas9-mediated gene editing to integrate a tandem-affinity (TAP) epitope tag into the genomic locus of HSC70. This system offers several benefits over existing expression systems including native expression, no requirement for selection, and homogeneity between cells. This cell line, freely available to chaperone researchers, will aid in small and large-scale protein interaction studies as well as the study of biochemical activities and structure-function relationships of the Hsc70 protein.
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Affiliation(s)
- Nitika
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, 28223, USA
| | - Andrew W Truman
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, 28223, USA.
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Kita K, Shiota M, Tanaka M, Otsuka A, Matsumoto M, Kato M, Tamada S, Iwao H, Miura K, Nakatani T, Tomita S. Heat shock protein 70 inhibitors suppress androgen receptor expression in LNCaP95 prostate cancer cells. Cancer Sci 2017; 108:1820-1827. [PMID: 28691182 PMCID: PMC5581527 DOI: 10.1111/cas.13318] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/31/2022] Open
Abstract
Androgen deprivation therapy is initially effective for treating patients with advanced prostate cancer; however, the prostate cancer gradually becomes resistant to androgen deprivation therapy, which is termed castration-resistant prostate cancer (CRPC). Androgen receptor splice variant 7 (AR-V7), one of the causes of CRPC, is correlated with resistance to a new-generation AR antagonist (enzalutamide) and poor prognosis. Heat shock protein 70 (Hsp70) inhibitor is known to decrease the levels of full-length AR (AR-FL), but little is known about its effects against CRPC cells expressing AR-V7. In this study, we investigated the effect of the Hsp70 inhibitors quercetin and VER155008 in the prostate cancer cell line LNCaP95 that expresses AR-V7, and explored the mechanism by which Hsp70 regulates AR-FL and AR-V7 expression. Quercetin and VER155008 decreased cell proliferation, increased the proportion of apoptotic cells, and decreased the protein levels of AR-FL and AR-V7. Furthermore, VER155008 decreased AR-FL and AR-V7 mRNA levels. Immunoprecipitation with Hsp70 antibody and mass spectrometry identified Y-box binding protein 1 (YB-1) as one of the molecules regulating AR-FL and AR-V7 at the transcription level through interaction with Hsp70. VER155008 decreased the phosphorylation of YB-1 and its localization in the nucleus, indicating that the involvement of Hsp70 in AR regulation might be mediated through the activation and nuclear translocation of YB-1. Collectively, these results suggest that Hsp70 inhibitors have potential anti-tumor activity against CRPC by decreasing AR-FL and AR-V7 expression through YB-1 suppression.
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Affiliation(s)
- Kazuaki Kita
- Department of UrologyOsaka City University Medical SchoolOsakaJapan
| | - Masayuki Shiota
- Department of PharmacologyOsaka City University Medical SchoolOsakaJapan
- Department of Research Support PlatformOsaka City University Medical SchoolOsakaJapan
| | - Masako Tanaka
- Department of Applied Pharmacology and TherapeuticsOsaka City University Medical SchoolOsakaJapan
| | - Asuka Otsuka
- Department of Applied Pharmacology and TherapeuticsOsaka City University Medical SchoolOsakaJapan
| | - Masaki Matsumoto
- Department of Molecular and Cellular BiologyMedical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Minoru Kato
- Department of UrologyOsaka City University Medical SchoolOsakaJapan
| | - Satoshi Tamada
- Department of UrologyOsaka City University Medical SchoolOsakaJapan
| | | | - Katsuyuki Miura
- Department of Applied Pharmacology and TherapeuticsOsaka City University Medical SchoolOsakaJapan
| | - Tatsuya Nakatani
- Department of UrologyOsaka City University Medical SchoolOsakaJapan
| | - Shuhei Tomita
- Department of PharmacologyOsaka City University Medical SchoolOsakaJapan
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Takahashi K, Tanaka M, Yashiro M, Matsumoto M, Ohtsuka A, Nakayama KI, Izumi Y, Nagayama K, Miura K, Iwao H, Shiota M. Protection of stromal cell-derived factor 2 by heat shock protein 72 prevents oxaliplatin-induced cell death in oxaliplatin-resistant human gastric cancer cells. Cancer Lett 2016; 378:8-15. [PMID: 27157913 DOI: 10.1016/j.canlet.2016.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 01/03/2023]
Abstract
Heat shock protein 72 (Hsp72) is a molecular chaperone that assists in the folding of nascent polypeptides and in the refolding of denatured proteins. In many cancers, Hsp72 is constitutively expressed at elevated levels, which can result in enhanced stress tolerance. Similarly, following treatment with anticancer drugs, Hsp72 binds to denatured proteins that may be essential for survival. We therefore hypothesized that Hsp72 client proteins may play a crucial role in drug resistance. Here, we aimed to identify proteins that are critical for oxaliplatin (OXA) resistance by analyzing human gastric cancer cell lines, as well as OXA-resistant cells via a mass spectrometry-based proteomic approach combined with affinity purification using anti-Hsp72 antibodies. Stromal cell-derived factor 2 (SDF-2) was identified as an Hsp72 client protein unique to OCUM-2M/OXA cells. SDF-2 was overexpressed in OXA-resistant cells and SDF-2 silencing promoted the apoptotic effects of OXA. Furthermore, Hsp72 prevented SDF-2 degradation in a chaperone activity-dependent manner. Together, our data demonstrate that Hsp72 protected SDF-2 to avoid OXA-induced cell death. We propose that inhibition of SDF-2 may comprise a novel therapeutic strategy to counteract OXA-resistant cancers.
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Affiliation(s)
- Katsuyuki Takahashi
- Department of Pharmacology, Osaka City University Medical School, Osaka, Japan; Department of Pharmacy, Osaka City University Hospital, Osaka, Japan
| | - Masako Tanaka
- Applied Pharmacology and Therapeutics, Osaka City University Medical School, Osaka, Japan
| | - Masakazu Yashiro
- Oncology Institute of Geriatrics and Medical Science, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Asuka Ohtsuka
- Applied Pharmacology and Therapeutics, Osaka City University Medical School, Osaka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yasukatsu Izumi
- Department of Pharmacology, Osaka City University Medical School, Osaka, Japan
| | - Katsuya Nagayama
- Department of Pharmacy, Osaka City University Hospital, Osaka, Japan
| | - Katsuyuki Miura
- Department of Pharmacology, Osaka City University Medical School, Osaka, Japan; Applied Pharmacology and Therapeutics, Osaka City University Medical School, Osaka, Japan
| | - Hiroshi Iwao
- Department of Pharmacology, Osaka City University Medical School, Osaka, Japan
| | - Masayuki Shiota
- Department of Pharmacology, Osaka City University Medical School, Osaka, Japan.
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