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Joshi U, Pandya M, Gupta S, George LB, Highland H. Extracellular Proteomic Profiling from the Erythrocytes Infected with Plasmodium Falciparum 3D7 Holds Promise for the Detection of Biomarkers. Protein J 2024:10.1007/s10930-024-10212-1. [PMID: 39009910 DOI: 10.1007/s10930-024-10212-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2024] [Indexed: 07/17/2024]
Abstract
Plasmodium falciparum (P. falciparum), which causes the most severe form of malaria, if left untreated, has 24 h window in which it can cause severe illness and even death. The aim of this study was to create the most comprehensive and informative secretory-proteome possible by combining high-accuracy and high-sensitivity protein identification technology. In this study, we used Plasmodium falciparum 3D7 (Pf3D7) as the model parasite to develop a label-free quantification proteomic strategy with the main goal of identifying Pf3D7 proteins that are supposed to be secreted outside the infected erythrocytes in the spent media culture during the in-vitro study. The spent culture media supernatant was subjected to differential and ultra-centrifugation steps followed by total protein extraction, estimation, and in-solution digestion using trypsin, digested peptides were analyzed using Nano-LC coupled with ESI for MS/MS. MS/MS spectra were processed using Maxquant software (v2.1.4.0.). Non-infected erythrocytes incubated spent cultured media supernatant were considered as control. Out of discovered 38 proteins, proteins belonging to P. falciparum spp. were EGF-like protein (C0H544), Endoplasmic reticulum chaperone GRP170 (C0H5H0), Small GTP-binding protein sar1 (Q8I1S0), Erythrocyte membrane protein 1, PfEMP1 (Q8I639), aldehyde reductase (Q8ID61), Conserved Plasmodium proteins (Q8IEH3, Q8ILD1), Antigen 332, DBL-like protein (Q8IHN4), Fe-S cluster assembly protein (Q8II78), identified and chosen for further in-depth investigation. This study highlights the value of secretory Plasmodium proteins play crucial roles in various aspects of the disease progression and host-pathogen interactions which can serve as diagnostic markers for malaria infection.
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Affiliation(s)
- Urja Joshi
- Department of Biochemistry, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India.
- Department of Zoology, BMTC, Human Genetics and WLC, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India.
| | - Maulik Pandya
- Department of Botany, Bioinformatics and Climate change, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Sharad Gupta
- Biological Engineering, IIT Gandhinagar, Palaj, Gujarat, India
| | - Linz-Buoy George
- Department of Zoology, BMTC, Human Genetics and WLC, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Hyacinth Highland
- Department of Zoology, BMTC, Human Genetics and WLC, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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2
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Gu H, Li J. Mathematical model of ion chronogram from in-tube solid-phase microextraction device coupled with mass spectrometry and optimization framework. J Chromatogr A 2024; 1731:465167. [PMID: 39033707 DOI: 10.1016/j.chroma.2024.465167] [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: 04/20/2024] [Revised: 07/08/2024] [Accepted: 07/13/2024] [Indexed: 07/23/2024]
Abstract
A mathematical description and experimental outputs exhibited that an ion chronogram from an in-tube solid-phase microextraction (SPME) device linked with mass spectrometry (in-tube-SPME-MS) generally appears as a right-skew unimodal signal with a heavy right tail. Analogous to liquid chromatography coupled with mass spectrometry (LC-MS), in-tube-SPME-MS can utilize the area under its produced ion chronogram for regression analysis and has been shown to be a potential approach for fast quantification of analyte. Different level of unimodity of signal in the ion chronogram could positively or negatively affect the choice of the area used for quantification and finally impact on analysis sensitivity and time efficiency of in-tube-SPME-MS. In the paper, we showed that different in-tube SPME design choices and elution experimental setups produce ion chronograms with controllable varying unimodal peak shape patterns. An improved mathematical model was built based on the plate theory of chromatography and the Van Deemter equation to quantitatively describe the elution process from in-tube-SPME device. A computer simulation was implemented to predict ion chronograms and the results were compared with experimental ion chronograms to show the effectiveness of the model. An optimization framework was further presented based on the model to identify optimal device designs (length and diameter of device) and experimental parameters (flow rate) to track targeted ion chronograms with "desired" peak shape patterns. Empirical elution experiments with the in-tube SPME devices adopting optimized geometric parameters and optimal experimental setups confirmed the consistency between the experimental ion chronograms and the numerical simulations to a certain level.
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Affiliation(s)
- Hao Gu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Jiwen Li
- Hanbot Institute, Yovole Networks Inc., Shanghai 200433, China.
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3
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Zhu G, Wang L, Wang X, Dong X, Yang S, Wang J, Xu S, Zeng Y. Comparative Proteomics Identified EXOSC1 as a Target Protein of Anticancer Peptide LVTX-8 in Nasopharyngeal Carcinoma Cells. J Proteome Res 2024. [PMID: 38700954 DOI: 10.1021/acs.jproteome.4c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Nasopharyngeal carcinoma (NPC) is a prevalent malignancy that usually occurs among the nose and throat. Due to mild initial symptoms, most patients are diagnosed in the late stage, and the recurrence rate of tumors is high, resulting in many deaths every year. Traditional radiotherapy and chemotherapy are prone to causing drug resistance and significant side effects. Therefore, searching for new bioactive drugs including anticancer peptides is necessary and urgent. LVTX-8 is a peptide toxin synthesized from the cDNA library of the spider Lycosa vittata, which is consisting of 25 amino acids. In this study, a series of in vitro cell experiments such as cell toxicity, colony formation, and cell migration assays were performed to exam the anticancer activity of LVTX-8 in NPC cells (5-8F and CNE-2). The results suggested that LVTX-8 significantly inhibited cell proliferation and migration of NPC cells. To find the potential molecular targets for the anticancer capability of LVTX-8, high-throughput proteomic and bioinformatics analysis were conducted on NPC cells. The results identified EXOSC1 as a potential target protein with significantly differential expression levels under LVTX-8+/LVTX-8- conditions. The results in this research indicate that spider peptide toxin LVTX-8 exhibits significant anticancer activity in NPC, and EXOSC1 may serve as a target protein for its anticancer activity. These findings provide a reference for the development of new therapeutic drugs for NPC and offer new ideas for the discovery of biomarkers related to NPC diagnosis. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (https://proteomecentral.proteomexchange.org) via the iProX partner repository with the data set identifier PXD050542.
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Affiliation(s)
- Ganghua Zhu
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Lingxiang Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
| | - Xingyao Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
| | - Xiaoping Dong
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
| | - Shu Yang
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Jiaqi Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
| | - Siyuan Xu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
| | - Yong Zeng
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
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4
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Gu H, Li J, Liang Q, Xu W. Solid phase microextraction device coupled with miniature mass spectrometry and mathematical model of its ion chronogram. Talanta 2024; 271:125651. [PMID: 38262130 DOI: 10.1016/j.talanta.2024.125651] [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: 11/09/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/25/2024]
Abstract
Modern solid phase microextraction (SPME) device linked with mass spectrometry (SPME-MS) has evolved from producing ion chronogram as flat noisy signal to as unimodal-like signal. We designed a SPME device, which is closer in morphology to LC column, linked it with a miniature mass spectrometer (SPME-Mini MS), and proposed a mathematical model that elution of compound from the SPME device is equivalent to overlay of elution of the compound from the infinite LC columns with the lengths between 0 and the length of the device and it can generate an ion chronogram as right-skew unimodal signal. Rhodamine B as analyte was used for experimental verification and its unimodal signal was used to fit the parameters of a computer simulation program based on the model. The experimental results and simulations empirically cross-confirmed that SPME-Mini MS can generate ion chronogram as clean right-skew unimodal signal. Furthermore, the SPME-Mini MS system was used for quantitative analysis of psychotropic drugs (i.e. risperidone and aripiprazole) in artificial urine. The results preliminarily demonstrated that the system can utilize area under unimodal signal for quantitative analysis and has potential to be applied for on-site, fast and accurate quantification of drugs and other compounds.
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Affiliation(s)
- Hao Gu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Jiwen Li
- Hanbot Institute, Yovole Networks Inc, Shanghai, 200433, China.
| | - Qiong Liang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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5
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Lan XY, Li D, Cui Y, Nguyen TN, Li S, Chen HS. Proteomic analysis of jugular venous blood in acute large vessel occlusion stroke with futile recanalization. J Cereb Blood Flow Metab 2024; 44:702-711. [PMID: 38000017 PMCID: PMC11197136 DOI: 10.1177/0271678x231216767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/13/2023] [Accepted: 10/17/2023] [Indexed: 11/26/2023]
Abstract
Futile recanalization (FR) after endovascular treatment (EVT) remains a significant challenge for acute ischemic stroke (AIS) with large vessel occlusion (LVO). The pathogenesis of FR has not been well elucidated. We prospectively enrolled anterior circulation LVO-AIS patients who achieved successful recanalization after EVT. The jugular venous blood ipsilateral to stroke was collected before and immediately after recanalization. Plasma proteomic analysis based on liquid chromatography-mass spectrometry was performed using data-independent acquisition method. Differentially expressed proteins (DEPs) among patients with or without FR in the whole or propensity score matching (PSM) cohorts were screened according to the absolute value of fold change ≥1.5 and P value <0.05. We identified 104 and 34 DEPs between patients with or without FR in the whole cohort and PSM cohort, respectively. Bioinformatic analysis indicated that the identified proteins were primarily related to specific biological processes including immune response, complement activation, oxidative stress, lipid metabolism, protein ubiquitylation as well as autophagy, suggesting that these may be mechanisms in FR pathogenesis. Collectively, we discovered proteins that may be potential research targets for FR. The combination of proteomic and bioinformatic analysis could provide a better understanding of the pathogenesis of FR in a comprehensive manner.
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Affiliation(s)
- Xiao-Yan Lan
- Graduate School, Dalian Medical University, Dalian, China
- Department of Neurology, General Hospital of Northern Theater Command, Shenyang, China
- Department of Neurointervention, Dalian Municipal Central Hospital, Dalian, China
| | - Di Li
- Department of Neurointervention, Dalian Municipal Central Hospital, Dalian, China
| | - Yu Cui
- Department of Neurology, General Hospital of Northern Theater Command, Shenyang, China
| | - Thanh N Nguyen
- Department of Neurology, Radiology, Boston Medical Center, Boston, Massachusetts, USA
| | - Shen Li
- Department of Neurology and Psychiatry, Beijing Shijitan Hospital, Beijing, China
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing, China
| | - Hui-Sheng Chen
- Graduate School, Dalian Medical University, Dalian, China
- Department of Neurology, General Hospital of Northern Theater Command, Shenyang, China
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Wang J, Wang Z, Wang Q, Li X, Guo Y. Ubiquitous protein lactylation in health and diseases. Cell Mol Biol Lett 2024; 29:23. [PMID: 38317138 PMCID: PMC10845568 DOI: 10.1186/s11658-024-00541-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
For decades, lactate has been considered a byproduct of glycolysis. The lactate shuttle hypothesis shifted the lactate paradigm, demonstrating that lactate not only plays important roles in cellular metabolism but also cellular communications, which can transcend compartment barriers and can occur within and among different cells, tissues and organs. Recently, the discovery that lactate can induce a novel post-translational modification, named lysine lactylation (Kla), brings forth a new avenue to study nonmetabolic functions for lactate, which has inspired a 'gold rush' of academic and commercial interest. Zhang et al. first showed that Kla is manifested in histones as epigenetic marks, and then mounting evidences demonstrated that Kla also occurs in diverse non-histone proteins. The widespread Kla faithfully orchestrates numerous biological processes, such as transcription, metabolism and inflammatory responses. Notably, dysregulation of Kla touches a myriad of pathological processes. In this review, we comprehensively reviewed and curated the existing literature to retrieve the new identified Kla sites on both histones and non-histone proteins and summarized recent major advances toward its regulatory mechanism. We also thoroughly investigated the function and underlying signaling pathway of Kla and comprehensively summarize how Kla regulates various biological processes in normal physiological states. In addition, we also further highlight the effects of Kla in the development of human diseases including inflammation response, tumorigenesis, cardiovascular and nervous system diseases and other complex diseases, which might potentially contribute to deeply understanding and interpreting the mechanism of its pathogenicity.
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Affiliation(s)
- Junyong Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou, 450001, Henan, China
- Center for Basic Medical Research, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Ziyi Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou, 450001, Henan, China
- Center for Basic Medical Research, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Qixu Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou, 450001, Henan, China
- Center for Basic Medical Research, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiao Li
- Department of Gastroenterology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450001, Henan, China
| | - Yaping Guo
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou, 450001, Henan, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, 450001, Henan, China.
- Center for Basic Medical Research, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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7
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Wang F, Zhang H, He B, Liu Z, Wu X, Liu Y, Xu X, Gou X, Wang H, Yang Q. Heat shock protein 90 inhibitors induce cell differentiation via the ubiquitin-dependent aurora kinase A degradation in a MPLW515L mouse model of primary myelofibrosis. Hematol Oncol 2023; 41:474-486. [PMID: 36422297 DOI: 10.1002/hon.3110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
Primary myelofibrosis (PMF) is characterized by immature megakaryocytic hyperplasia, splenomegaly, extramedullary hematopoiesis and bone marrow fibrosis. Our preclinical study had demonstrated that aurora kinase A (AURKA) inhibitor MLN8237 reduced the mutation burden of PMF by inducing differentiation of immature megakaryocytes. However, it only slightly alleviated splenomegaly, reduced tissue fibrosis, and normalized megakaryocytes in PMF patients of the preliminary clinical study. So enhancing therapeutic efficacy of PMF is needed. In this study, we found that AURKA directly interacted with heat shock protein 90 (HSP90) and HSP90 inhibitors promoted the ubiquitin-dependent AURKA degradation. We demonstrated that HSP90 inhibitors 17-allylamino-17-demethoxygeldanamycin (17-AAG) and 17-dimethylaminoethylamino-17-demethoxygeldanamycin (17-DMAG), normalized peripheral blood counts, improved splenomegaly, attenuated extramedullary hematopoiesis, decreased tissue fibrosis and reduced mutant burden in a MPLW515L mouse model of PMF. Importantly, both 17-AAG and 17-DMAG treatment at effective doses in vivo did not influence on hematopoiesis in healthy mice. Collectively, the study demonstrates that HSP90 inhibitors induce cell differentiation via the ubiquitin-dependent AURKA and also are safe and effective for the treatment of a MPLW515L mouse model of PMF, which may provide a new strategy for PMF therapy. Further, we demonstrate that combined therapy shows superior activity in acute megakaryocytic leukemia mouse model than single therapy.
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Affiliation(s)
- Fuping Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Haotian Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Binghong He
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Zihan Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xinxin Wu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yuankai Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xin Xu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xiaoxue Gou
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Haitao Wang
- Department of Hematology, Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qiong Yang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
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8
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Li X, Bi H. A strategy to link the changes in the quality traits of Japanese sea bass ( Lateolabrax japonicus) muscle and proteins in its exudate during cold storage using mass spectrometry. Analyst 2023; 148:1235-1245. [PMID: 36794760 DOI: 10.1039/d3an00060e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this study, Japanese sea bass (Lateolabrax japonicus) was used as a model to link the changes in the quality traits of fish muscle during storage to the change of protein in muscle exudate. Matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) combined with variables importance in projection (VIP) analysis, and high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), were applied to identify the proteins by analyzing the enzymatic hydrolysates of exudates of fish muscle. The link in the identified proteins to the change in the quality traits of fish muscle during storage was explored using pyramid diagrams. Nine proteins were identified from the exudate of Japanese sea bass muscle during 12 days of storage at 4 °C. Of these, four proteins, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), heat shock protein 90 (HSP90), and peroxiredoxin 1 (PRX1), and beta-actin were found to be responsible for the changes in the quality traits of fish muscle. It is promising to correlate the changes in the quality traits of fish muscle and proteins in muscle exudate via MS-based protein identification and the construction of a relationship diagram to understand the mechanism of muscle change at the molecular level.
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Affiliation(s)
- Xiaoxia Li
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, 201306 Shanghai, China.
| | - Hongyan Bi
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, 201306 Shanghai, China.
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9
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Xue Z, Zeng J, Yin X, Li Y, Meng B, Zhao Y, Fang X, Gong X, Dai X. Investigation on acquired palbociclib resistance by LC-MS based multi-omics analysis. Front Mol Biosci 2023; 10:1116398. [PMID: 36743215 PMCID: PMC9892630 DOI: 10.3389/fmolb.2023.1116398] [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: 12/05/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
Palbociclib is a specific CDK4/6 inhibitor that has been widely applied in multiple types of tumors. Different from cytotoxic drugs, the anticancer mechanism of palbociclib mainly depends on cell cycle inhibition. Therefore, the resistance mechanism is different. For clinical cancer patients, drug resistance is inevitable for almost all cancer therapies including palbociclib. We have trained palbociclib resistant cells in vitro to simulate the clinical situation and applied LC-MS multi-omics analysis methods including proteomic, metabolomic, and glycoproteomic techniques, to deeply understand the underly mechanism behind the resistance. As a result of proteomic analysis, the resistant cells were found to rely on altered metabolic pathways to keep proliferation. Metabolic processes related to carbohydrates, lipids, DNA, cellular proteins, glucose, and amino acids were observed to be upregulated. Most dramatically, the protein expressions of COX-1 and NDUFB8 have been detected to be significantly overexpressed by proteomic analysis. When a COX-1 inhibitor was hired to combine with palbociclib, a synergistic effect could be obtained, suggesting the altered COX-1 involved metabolic pathway is an important reason for the acquired palbociclib resistance. The KEGG pathway of N-glycan biosynthesis was identified through metabolomics analysis. N-glycoproteomic analysis was therefore included and the global glycosylation was found to be elevated in the palbociclib-resistant cells. Moreover, integration analysis of glycoproteomic data allowed us to detect a lot more proteins that have been glycosylated with low abundances, these proteins were considered to be overwhelmed by those highly abundant proteins during regular proteomic LC-MS detection. These low-abundant proteins are mainly involved in the cellular biology processes of cell migration, the regulation of chemotaxis, as well as the glycoprotein metabolic process which offered us great more details on the roles played by N-glycosylation in drug resistance. Our result also verified that N-glycosylation inhibitors could enhance the cell growth inhibition of palbociclib in resistant cells. The high efficiency of the integrated multi-omics analysis workflow in discovering drug resistance mechanisms paves a new way for drug development. With a clear understanding of the resistance mechanism, new drug targets and drug combinations could be designed to resensitize the resistant tumors.
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Affiliation(s)
- Zhichao Xue
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Jiaming Zeng
- College of Chemical Engineering, Shenyang University of Chemical Technology, Shenyang, China
| | - Xinchi Yin
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yongshu Li
- Shenzhen Institute for Technology Innovation, National Institute of Metrology Shenzhen, Shenzhen, China
| | - Bo Meng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yang Zhao
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China,*Correspondence: Xiaoyun Gong, ; Xinhua Dai,
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China,*Correspondence: Xiaoyun Gong, ; Xinhua Dai,
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10
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Nisar N, Mir SA, Kareem O, Pottoo FH. Proteomics approaches in the identification of cancer biomarkers and drug discovery. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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11
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Jiang F, Zhang C, Lu Z, Liu J, Liu P, Huang M, Zhong G. Simultaneous absolute protein quantification of seven cytochrome P450 isoforms in rat liver microsomes by LC-MS/MS-based isotope internal standard method. Front Pharmacol 2022; 13:906027. [PMID: 36059965 PMCID: PMC9428253 DOI: 10.3389/fphar.2022.906027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
The cytochrome P450 (CYP) enzymes play a pivotal role in drug metabolism. LC-MS/MS-based targeting technology has been applied to the analysis of CYP enzymes, promoting drug development and drug-drug interaction studies. Rat is one of the most commonly used models for drug metabolism assessment, but LC-MS/MS assay quantifying the abundance of CYP enzymes in rats is rarely reported. Herein, an accurate and stable LC-MS/MS based method was developed and validated for the simultaneous quantification of seven major rat CYP isoforms (CYP1A2, 2B1, 2C6, 2C11, 2D1, 2E1, and 3A1) in liver microsomes. The careful optimization of trypsin digestion and chromatography combined with isotope-labeled peptide as internal standard improved the efficiency and accuracy of the analysis. Highly specific surrogate peptides were obtained by a procedure including trypsin digestion for six hours and separated on a Hypersil Gold C18 column (100 × 2.1 mm, 3 μm) using gradient elution for 15 min with a mobile phase of water containing 0.1% formic acid and acetonitrile. In the method validation, linearity, matrix effect, recovery, stability, accuracy, and precision all meet the requirements. Subsequently, this method was applied to detect seven enzymes in rat liver microsomes from four different sources, and the correlation between the abundance and activity of CYP enzymes was further analyzed. The high-throughput detection method provided in this study will provide support for pertinent pharmaceutical research based on rat models.
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Affiliation(s)
- Fulin Jiang
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chang Zhang
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zihan Lu
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jingyu Liu
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiqing Liu
- School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-sen University, Guangzhou, China
| | - Min Huang
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Min Huang, ; Guoping Zhong,
| | - Guoping Zhong
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Min Huang, ; Guoping Zhong,
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Wen XP, Long G, Zhang YZ, Huang H, Liu TH, Wan QQ. Identification of different proteins binding to Na, K-ATPase α1 in LPS-induced ARDS cell model by proteomic analysis. Proteome Sci 2022; 20:10. [PMID: 35681168 PMCID: PMC9178877 DOI: 10.1186/s12953-022-00193-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
Background Acute respiratory distress syndrome (ARDS) is characterized by refractory hypoxemia caused by accumulation of pulmonary fluid, which is related to inflammatory cell infiltration, impaired tight junction of pulmonary epithelium and impaired Na, K-ATPase function, especially Na, K-ATPase α1 subunit. Up until now, the pathogenic mechanism at the level of protein during lipopolysaccharide- (LPS-) induced ARDS remains unclear. Methods Using an unbiased, discovery and quantitative proteomic approach, we discovered the differentially expressed proteins binding to Na, K-ATPase α1 between LPS-A549 cells and Control-A549 cells. These Na, K-ATPase α1 interacting proteins were screened by co-immunoprecipitation (Co-IP) technology. Among them, some of the differentially expressed proteins with significant performance were identified and quantified by liquid chromatography-tandem mass spectrometry (LC–MS/MS). Data are available via ProteomeXchange with identifier PXD032209. The protein interaction network was constructed by the related Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Several differentially expressed proteins were validated by Western blot. Results Of identified 1598 proteins, 89 were differentially expressed proteins between LPS-A549 cells and Control-A549 cells. Intriguingly, protein–protein interaction network showed that there were 244 significantly enriched co-expression among 60 proteins in the group control-A549. while the group LPS-A549 showed 43 significant enriched interactions among 29 proteins. The related GO and KEGG analysis found evident phenomena of ubiquitination and deubiquitination, as well as the pathways related to autophagy. Among proteins with rich abundance, there were several intriguing ones, including the deubiquitinase (OTUB1), the tight junction protein zonula occludens-1 (ZO-1), the scaffold protein in CUL4B-RING ubiquitin ligase (CRL4B) complexes (CUL4B) and the autophagy-related protein sequestosome-1 (SQSTM1). Conclusions In conclusion, our proteomic approach revealed targets related to the occurrence and development of ARDS, being the first study to investigate significant differences in Na, K-ATPase α1 interacting proteins between LPS-induced ARDS cell model and control-A549 cell. These proteins may help the clinical diagnosis and facilitate the personalized treatment of ARDS. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12953-022-00193-3.
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Affiliation(s)
- Xu-Peng Wen
- Transplantation Center, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Guo Long
- Respiratory ICU, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Yue-Zhong Zhang
- Clinical Medicine, Xiangya School of Medicine, Central South University, Changsha, 410083, China
| | - He Huang
- Hunan International Travel Health Care Center, Changsha, 410001, Hunan, China
| | - Tao-Hua Liu
- Clinical Medicine, Xiangya School of Medicine, Central South University, Changsha, 410083, China
| | - Qi-Quan Wan
- Transplantation Center, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
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13
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Lai Y, Chu X, Di L, Gao W, Guo Y, Liu X, Lu C, Mao J, Shen H, Tang H, Xia CQ, Zhang L, Ding X. Recent advances in the translation of drug metabolism and pharmacokinetics science for drug discovery and development. Acta Pharm Sin B 2022; 12:2751-2777. [PMID: 35755285 PMCID: PMC9214059 DOI: 10.1016/j.apsb.2022.03.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 02/08/2023] Open
Abstract
Drug metabolism and pharmacokinetics (DMPK) is an important branch of pharmaceutical sciences. The nature of ADME (absorption, distribution, metabolism, excretion) and PK (pharmacokinetics) inquiries during drug discovery and development has evolved in recent years from being largely descriptive to seeking a more quantitative and mechanistic understanding of the fate of drug candidates in biological systems. Tremendous progress has been made in the past decade, not only in the characterization of physiochemical properties of drugs that influence their ADME, target organ exposure, and toxicity, but also in the identification of design principles that can minimize drug-drug interaction (DDI) potentials and reduce the attritions. The importance of membrane transporters in drug disposition, efficacy, and safety, as well as the interplay with metabolic processes, has been increasingly recognized. Dramatic increases in investments on new modalities beyond traditional small and large molecule drugs, such as peptides, oligonucleotides, and antibody-drug conjugates, necessitated further innovations in bioanalytical and experimental tools for the characterization of their ADME properties. In this review, we highlight some of the most notable advances in the last decade, and provide future perspectives on potential major breakthroughs and innovations in the translation of DMPK science in various stages of drug discovery and development.
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Affiliation(s)
- Yurong Lai
- Drug Metabolism, Gilead Sciences Inc., Foster City, CA 94404, USA
| | - Xiaoyan Chu
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Li Di
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Wei Gao
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Yingying Guo
- Eli Lilly and Company, Indianapolis, IN 46221, USA
| | - Xingrong Liu
- Drug Metabolism and Pharmacokinetics, Biogen, Cambridge, MA 02142, USA
| | - Chuang Lu
- Drug Metabolism and Pharmacokinetics, Accent Therapeutics, Inc. Lexington, MA 02421, USA
| | - Jialin Mao
- Department of Drug Metabolism and Pharmacokinetics, Genentech, A Member of the Roche Group, South San Francisco, CA 94080, USA
| | - Hong Shen
- Drug Metabolism and Pharmacokinetics Department, Bristol-Myers Squibb Company, Princeton, NJ 08540, USA
| | - Huaping Tang
- Bioanalysis and Biomarkers, Glaxo Smith Kline, King of the Prussia, PA 19406, USA
| | - Cindy Q. Xia
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co., Cambridge, MA 02139, USA
| | - Lei Zhang
- Office of Research and Standards, Office of Generic Drugs, CDER, FDA, Silver Spring, MD 20993, USA
| | - Xinxin Ding
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
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Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules 2022; 27:molecules27082411. [PMID: 35458608 PMCID: PMC9031286 DOI: 10.3390/molecules27082411] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.
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15
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Du S, Liang C, Sun Y, Ma B, Gao W, Geng W. The Attenuating Effect of Low-Intensity Pulsed Ultrasound on Hypoxia-Induced Rat Chondrocyte Damage in TMJ Osteoarthritis Based on TMT Labeling Quantitative Proteomic Analysis. Front Pharmacol 2022; 12:752734. [PMID: 34970140 PMCID: PMC8712703 DOI: 10.3389/fphar.2021.752734] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Temporomandibular joint osteoarthritis (TMJOA) is a degenerative disease with a complex and multifactorial etiology. An increased intrajoint pressure or weakened penetration can exacerbate the hypoxic state of the condylar cartilage microenvironment. Our group previously simulated the hypoxic environment of TMJOA in vitro. Low-intensity pulsed ultrasound (LIPUS) stimulation attenuates chondrocyte matrix degradation via a hypoxia-inducible factor (HIF) pathway-associated mechanism, but the mode of action of LIPUS is currently poorly understood. Moreover, most recent studies investigated the pathological mechanisms of osteoarthritis, but no biomarkers have been established for assessing the therapeutic effect of LIPUS on TMJOA with high specificity, which results in a lack of guidance regarding clinical application. Here, tandem mass tag (TMT)-based quantitative proteomic technology was used to comprehensively screen the molecular targets and pathways affected by the action of LIPUS on chondrocytes under hypoxic conditions. A bioinformatic analysis identified 902 and 131 differentially expressed proteins (DEPs) in the <1% oxygen treatment group compared with the control group and in the <1% oxygen + LIPUS stimulation group compared with the <1% oxygen treatment group, respectively. The DEPs were analyzed by gene ontology (GO), KEGG pathway and protein-protein interaction (PPI) network analyses. By acting on extracellular matrix (ECM)-associated proteins, LIPUS increases energy production and activates the FAK signaling pathway to regulate cell biological behaviors. DEPs of interest were selected to verify the reliability of the proteomic results. In addition, this experiment demonstrated that LIPUS could upregulate chondrogenic factors (such as Sox9, Collagen Ⅱ and Aggrecan) and increase the mucin sulfate content. Moreover, LIPUS reduced the hydrolytic degradation of the ECM by decreasing the MMP3/TIMP1 ratio and vascularization by downregulating VEGF. Interestingly, LIPUS improved the migration ability of chondrocytes. In summary, LIPUS can regulate complex biological processes in chondrocytes under hypoxic conditions and alter the expression of many functional proteins, which results in reductions in hypoxia-induced chondrocyte damage. ECM proteins such as thrombospondin4, thrombospondin1, IL1RL1, and tissue inhibitors of metalloproteinase 1 play a central role and can be used as specific biomarkers determining the efficacy of LIPUS and viable clinical therapeutic targets of TMJOA.
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Affiliation(s)
- Sa Du
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Chao Liang
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Yujie Sun
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Bowen Ma
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Wenmo Gao
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Wei Geng
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
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16
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Data-independent acquisition (DIA): An emerging proteomics technology for analysis of drug-metabolizing enzymes and transporters. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 39:49-56. [PMID: 34906325 DOI: 10.1016/j.ddtec.2021.06.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/22/2021] [Accepted: 06/21/2021] [Indexed: 01/22/2023]
Abstract
Data-independent acquisition (DIA) proteomics is a recently-developed global mass spectrometry (MS)-based proteomics strategy. In a DIA method, precursor ions are isolated into pre-defined isolation windows and fragmented; all fragmented ions in each window are then analyzed by a high-resolution mass spectrometer. DIA proteomics analysis is characterized by a broad protein coverage, high reproducibility, and accuracy, and its combination with advances in other techniques such as sample preparation and computational data analysis could lead to further improvements in assay performances. DIA technology has been increasingly utilized in various proteomics studies, including quantifying drug-metabolizing enzymes and transporters. Quantitative proteomics study of drug-metabolizing enzymes and transporters could lead to a better understanding of pharmacokinetics and pharmacodynamics and facilitate drug development. This review summarizes the application of DIA technology in proteomic analysis of drug-metabolizing enzymes and transporters.
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El Biali M, Karch R, Philippe C, Haslacher H, Tournier N, Hacker M, Zeitlinger M, Schmidl D, Langer O, Bauer M. ABCB1 and ABCG2 Together Limit the Distribution of ABCB1/ABCG2 Substrates to the Human Retina and the ABCG2 Single Nucleotide Polymorphism Q141K (c.421C> A) May Lead to Increased Drug Exposure. Front Pharmacol 2021; 12:698966. [PMID: 34220523 PMCID: PMC8242189 DOI: 10.3389/fphar.2021.698966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/04/2021] [Indexed: 12/26/2022] Open
Abstract
The widely expressed and poly-specific ABC transporters breast cancer resistance protein (ABCG2) and P-glycoprotein (ABCB1) are co-localized at the blood-brain barrier (BBB) and have shown to limit the brain distribution of several clinically used ABCB1/ABCG2 substrate drugs. It is currently not known to which extent these transporters, which are also expressed at the blood-retinal barrier (BRB), may limit drug distribution to the human eye and whether the ABCG2 reduced-function single-nucleotide polymorphism (SNP) Q141K (c.421C > A) has an impact on retinal drug distribution. Ten healthy male volunteers (five subjects with the c.421CC and c.421CA genotype, respectively) underwent two consecutive positron emission tomography (PET) scans after intravenous injection of the model ABCB1/ABCG2 substrate [11C]tariquidar. The second PET scan was performed with concurrent intravenous infusion of unlabelled tariquidar to inhibit ABCB1 in order to specifically reveal ABCG2 function.In response to ABCB1 inhibition with unlabelled tariquidar, ABCG2 c.421C > A genotype carriers showed significant increases (as compared to the baseline scan) in retinal radiotracer influx K1 (+62 ± 57%, p = 0.043) and volume of distribution VT (+86 ± 131%, p = 0.043), but no significant changes were observed in subjects with the c.421C > C genotype. Our results provide the first evidence that ABCB1 and ABCG2 may together limit the distribution of systemically administered ABCB1/ABCG2 substrate drugs to the human retina. Functional redundancy between ABCB1 and ABCG2 appears to be compromised in carriers of the c.421C > A SNP who may therefore be more susceptible to transporter-mediated drug-drug interactions at the BRB than non-carriers.
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Affiliation(s)
- Myriam El Biali
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, VIE, Austria
| | - Rudolf Karch
- Centre for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, VIE, Austria
| | - Cécile Philippe
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, VIE, Austria
| | - Helmuth Haslacher
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, VIE, Austria
| | - Nicolas Tournier
- Laboratoire d'Imagerie Biomédicale Multimodale (BioMaps), CEA, CNRS, Inserm, Service Hospitalier Frédéric Joliot, Université Paris-Saclay, Orsay, France
| | - Marcus Hacker
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, VIE, Austria
| | - Markus Zeitlinger
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, VIE, Austria
| | - Doreen Schmidl
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, VIE, Austria
| | - Oliver Langer
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, VIE, Austria.,Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, VIE, Austria
| | - Martin Bauer
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, VIE, Austria
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Dhuria NV, Haro B, Kapadia A, Lobo KA, Matusow B, Schleiff MA, Tantoy C, Sodhi JK. Recent developments in predicting CYP-independent metabolism. Drug Metab Rev 2021; 53:188-206. [PMID: 33941024 DOI: 10.1080/03602532.2021.1923728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
As lead optimization efforts have successfully reduced metabolic liabilities due to cytochrome P450 (CYP)-mediated metabolism, there has been an increase in the frequency of involvement of non-CYP enzymes in the metabolism of investigational compounds. Although there have been numerous notable advancements in the characterization of non-CYP enzymes with respect to their localization, reaction mechanisms, species differences and identification of typical substrates, accurate prediction of non-CYP-mediated clearance, with a particular emphasis with the difficulties in accounting for any extrahepatic contributions, remains a challenge. The current manuscript comprehensively summarizes the recent advancements in the prediction of drug metabolism and the in vitro to in vitro extrapolation of clearance for substrates of non-CYP drug metabolizing enzymes.
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Affiliation(s)
- Nikhilesh V Dhuria
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bianka Haro
- School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Amit Kapadia
- California Poison Control Center, University of California San Francisco, San Diego, CA, USA
| | | | - Bernice Matusow
- Department of Drug Metabolism and Pharmacokinetics, Plexxikon Inc, Berkeley, CA, USA
| | - Mary A Schleiff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Christina Tantoy
- Department of Drug Metabolism and Pharmacokinetics, Plexxikon Inc, Berkeley, CA, USA
| | - Jasleen K Sodhi
- Department of Drug Metabolism and Pharmacokinetics, Plexxikon Inc, Berkeley, CA, USA.,Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, CA, USA
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Lee W, Koyama S, Morita K, Kiriake A, Kikuchi R, Chu X, Lee N, Scialis RJ, Shen H, Kimoto E, Tremaine L, Ishiguro N, Lotz R, Maeda K, Kusuhara H, Sugiyama Y. Cell-to-Medium Concentration Ratio Overshoot in the Uptake of Statins by Human Hepatocytes in Suspension, but Not in Monolayer: Kinetic Analysis Suggesting a Partial Loss of Functional OATP1Bs. AAPS JOURNAL 2020; 22:133. [PMID: 33063163 PMCID: PMC7561564 DOI: 10.1208/s12248-020-00512-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/15/2020] [Indexed: 01/16/2023]
Abstract
Suspended human hepatocytes (SHH) have long been used in assessing hepatic drug uptake, while plated human hepatocytes in short-term monolayer culture (PHH) have gained use in recent years. This study aimed to cross-evaluate SHH and PHH in measuring the hepatic uptake mediated by organic anion transporting polypeptide 1Bs (OATP1Bs). We compared the time courses of cell-to-medium (C/M) concentration ratios and initial uptake clearance values of the OATP1B substrates (pitavastatin, rosuvastatin, cerivastatin, pravastatin, dehydropravastatin, and SC-62807) between SHH and PHH. For all compounds except cerivastatin, the C/M ratios in SHH displayed an apparent overshoot (an initial increase followed by a decrease) during the 180-min uptake experiment, but not in PHH. Based on the literature evidence suggesting the possible internalization of OATP1Bs in primary hepatocytes, separate experiments measured the drug uptake after varying lengths of pre-incubation in the drug-free medium. The initial uptake clearances of pitavastatin and rosuvastatin declined in SHH beyond an apparent threshold time of 20-min drug-free pre-incubation, but not in PHH. Kinetic modeling quantitatively captured the decline in the active uptake clearance in SHH, and more than half of the active uptake clearances of pitavastatin and rosuvastatin were prone to loss during the 180-min uptake experiment. These results suggested a partial, time-delayed loss of the functional OATP1Bs in SHH upon prolonged incubation. Our results indicate that PHH is more appropriate for experiments where a prolonged incubation is required, such as estimation of unbound hepatocyte-to-medium concentration ratio (Kp,uu) at the steady-state.
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Affiliation(s)
- Wooin Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, South Korea
| | - Satoshi Koyama
- Sugiyama Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, Japan
| | - Kiyoe Morita
- Sugiyama Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, Japan
| | - Aya Kiriake
- Sugiyama Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, Japan
| | | | - Xiaoyan Chu
- Merck & Co., Inc, North Wales, Pennsylvania, USA
| | - Nora Lee
- Daewoong Pharmaceutical Co., Ltd, Seoul, South Korea
| | | | - Hong Shen
- Bristol Myers Squibb, Princeton, New Jersey, USA
| | - Emi Kimoto
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc, Groton, Connecticut, USA
| | - Larry Tremaine
- Tremaine DMPK Consulting LLC, Merritt Island, Florida, USA
| | - Naoki Ishiguro
- Pharmacokinetics and Non-Clinical Safety Department, Nippon Boehringer Ingelheim Co., Ltd, Kobe, Hyogo, Japan
| | - Ralf Lotz
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Kazuya Maeda
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroyuki Kusuhara
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Yuichi Sugiyama
- Sugiyama Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, Japan.
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