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Singh DK, Basit A, Rettie AE, Alade N, Thummel K, Prasad B. Characterization of Gla proteoforms and non-Gla peptides of gamma carboxylated proteins: Application to quantification of prothrombin proteoforms in human plasma. Anal Chim Acta 2023; 1284:341972. [PMID: 37996163 PMCID: PMC10789187 DOI: 10.1016/j.aca.2023.341972] [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: 07/13/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Gamma (γ) carboxylation is an essential post-translational modification in vitamin K-dependent proteins (VKDPs), involved in maintaining critical biological homeostasis. Alterations in the abundance or activity of these proteins have pharmacological and pathological consequences. Importantly, low levels of fully γ-carboxylated clotting factors increase plasma des-γ-carboxy precursors resulting in little or no biological activity. Therefore, it is important to characterize the levels of γ-carboxylation that reflect the active state of these proteins. The conventional enzyme-linked immunosorbent assay for protein induced by vitamin K absence or antagonist II (PIVKA-II) quantification uses an antibody that is not applicable to distinguish different γ-carboxylation states. Liquid chromatography-mass spectrometry (LC-MS) approaches have been utilized to distinguish different γ-carboxylated proteoforms, however, these attempts were impeded by poor sensitivity due to spontaneous neutral loss of CO2 and simultaneous cleavage of the backbone bond in the collision cell. In this study, we utilized an alkaline mobile phase in combination with polarity switching (positive and negative ionization modes) to simultaneously identify and quantify γ-carboxylated VKDPs. The method was applied to compare Gla proteomics of prothrombin (FII) in 10 μL plasma samples of healthy control and warfarin-treated adults. We also identified surrogate non-Gla peptides for seven other VKDPs to quantify total (active plus inactive) protein levels. The total protein approach (TPA) was used to quantify absolute levels of the VKDPs in human plasma.
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Affiliation(s)
- Dilip Kumar Singh
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Abdul Basit
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Nathan Alade
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Kenneth Thummel
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA.
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Urbaniak A, Thummel KE, Alade AN, Rettie AE, Prasad B, De Nicolò A, Martin JH, Sheppard DN, Jarvis MF. Experimental pharmacology in precision medicine. Pharmacol Res Perspect 2023; 11:e01147. [PMID: 37885364 PMCID: PMC10603287 DOI: 10.1002/prp2.1147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Affiliation(s)
- Alicja Urbaniak
- Department of Biochemistry and Molecular BiologyUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | | | - Ayoade N. Alade
- School of PharmacyUniversity of WashingtonSeattleWashingtonUSA
| | - Allan E. Rettie
- School of PharmacyUniversity of WashingtonSeattleWashingtonUSA
| | - Bhagwat Prasad
- Department of Pharmaceutical SciencesWashington State UniversitySpokaneWashingtonUSA
| | | | - Jennifer H. Martin
- The University of Newcastle Hunter Medical Research InstituteNew LambtonNew South WalesAustralia
| | - David N. Sheppard
- School of Physiology, Pharmacology and NeuroscienceUniversity of BristolBristolUK
| | - Michael F. Jarvis
- Pharmaceutical SciencesUniversity of Illinois‐ChicagoChicagoIllinoisUSA
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Hadi H, Wan Shuaib WMA, Raja Ali RA, Othman H. Utility of PIVKA-II and AFP in Differentiating Hepatocellular Carcinoma from Non-Malignant High-Risk Patients. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58081015. [PMID: 36013482 PMCID: PMC9416286 DOI: 10.3390/medicina58081015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022]
Abstract
Background and Objectives: We aim to compare the diagnostic performance of Protein induced by vitamin K absence-II (PIVKA-II), a biomarker for hepatocellular carcinoma (HCC), and alpha-fetoprotein (AFP) in differentiating HCC and non-malignant high-risk (NMHR) groups and to determine their cut-off values. Materials and Methods: A total of 163 patients, including 40 with HCC and 123 with NMHR (100 with liver cirrhosis and 23 with non-cirrhotic high-risk patients) were prospectively enrolled. The levels of AFP and PIVKA-II were measured, and their cut-off values were determined. We calculated and compared the areas under the receiver operating characteristic (AUROC) curves of PIVKA-II, AFP, and their combination. Results: The levels of PIVKA-II and AFP were found to be significantly higher in the HCC compared to NMHR patients (p < 0.0001). For the differentiation of HCC from NMHR, the optimal cutoff values for PIVKA-II and AFP were 36.7 mAU/mL (90% sensitivity; 82.1% specificity) and 14.2 ng/mL (75% sensitivity; 93.5% specificity), respectively. The AUROC of PIVKA-II (0.905, p < 0.0001) was higher compared to AFP (0.869, p < 0.0001), but the combination of PIVKA−II and AFP gave the highest AUROC value (0.911, p < 0.0001). However, their differences were not statistically significant (AFP vs. PIVKA; p = 0.4775, AFP vs. Combination; p = 0.3808, PIVKA vs. Combination; p = 0.2268). Conclusions: PIVKA-II and AFP showed equal performance in detecting HCC in high-risk patients. AFP as a screening marker for HCC may be adequate, and replacing or adding the PIVKA-II test in current clinical practice may be of little value.
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Affiliation(s)
- Hana Hadi
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Hospital Canselor Tuanku Muhriz UKM, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia; (H.H.); (H.O.)
| | - Wan Muhammad Azfar Wan Shuaib
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Hospital Canselor Tuanku Muhriz UKM, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia; (H.H.); (H.O.)
- Correspondence: ; Tel.: +603-9145-9502
| | - Raja Affendi Raja Ali
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Hospital Canselor Tuanku Muhriz UKM, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia;
| | - Hanita Othman
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Hospital Canselor Tuanku Muhriz UKM, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia; (H.H.); (H.O.)
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Ahire D, Kruger L, Sharma S, Mettu VS, Basit A, Prasad B. Quantitative Proteomics in Translational Absorption, Distribution, Metabolism, and Excretion and Precision Medicine. Pharmacol Rev 2022; 74:769-796. [PMID: 35738681 DOI: 10.1124/pharmrev.121.000449] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A reliable translation of in vitro and preclinical data on drug absorption, distribution, metabolism, and excretion (ADME) to humans is important for safe and effective drug development. Precision medicine that is expected to provide the right clinical dose for the right patient at the right time requires a comprehensive understanding of population factors affecting drug disposition and response. Characterization of drug-metabolizing enzymes and transporters for the protein abundance and their interindividual as well as differential tissue and cross-species variabilities is important for translational ADME and precision medicine. This review first provides a brief overview of quantitative proteomics principles including liquid chromatography-tandem mass spectrometry tools, data acquisition approaches, proteomics sample preparation techniques, and quality controls for ensuring rigor and reproducibility in protein quantification data. Then, potential applications of quantitative proteomics in the translation of in vitro and preclinical data as well as prediction of interindividual variability are discussed in detail with tabulated examples. The applications of quantitative proteomics data in physiologically based pharmacokinetic modeling for ADME prediction are discussed with representative case examples. Finally, various considerations for reliable quantitative proteomics analysis for translational ADME and precision medicine and the future directions are discussed. SIGNIFICANCE STATEMENT: Quantitative proteomics analysis of drug-metabolizing enzymes and transporters in humans and preclinical species provides key physiological information that assists in the translation of in vitro and preclinical data to humans. This review provides the principles and applications of quantitative proteomics in characterizing in vitro, ex vivo, and preclinical models for translational research and interindividual variability prediction. Integration of these data into physiologically based pharmacokinetic modeling is proving to be critical for safe, effective, timely, and cost-effective drug development.
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Affiliation(s)
- Deepak Ahire
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Laken Kruger
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Sheena Sharma
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Vijaya Saradhi Mettu
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Abdul Basit
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
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Li P, Du Y, Ma M, Zhang J. Nitrogen-doped graphene quantum dots coated with molecularly imprinted polymers as a fluorescent sensor for selective determination of warfarin. NEW J CHEM 2022. [DOI: 10.1039/d2nj00853j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The strong photoluminescence of NGQDs and the selectivity of MIPs were combined to construct a fluorescent sensor for rapid determination of warfarin.
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Affiliation(s)
- Peipei Li
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, P. R. China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Yingxiang Du
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, P. R. China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Mingxuan Ma
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, P. R. China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jian Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, P. R. China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
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Tsurusawa N, Chang J, Namba M, Makioka D, Yamura S, Iha K, Kyosei Y, Watabe S, Yoshimura T, Ito E. Modified ELISA for Ultrasensitive Diagnosis. J Clin Med 2021; 10:5197. [PMID: 34768717 PMCID: PMC8585087 DOI: 10.3390/jcm10215197] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
An enzyme-linked immunosorbent assay (ELISA) can be used for quantitative measurement of proteins, and improving the detection sensitivity to the ultrasensitive level would facilitate the diagnosis of various diseases. In the present review article, we first define the term 'ultrasensitive'. We follow this with a survey and discussion of the current literature regarding modified ELISA methods with ultrasensitive detection and their application for diagnosis. Finally, we introduce our own newly devised system for ultrasensitive ELISA combined with thionicotinamide adenine dinucleotide cycling and its application for the diagnosis of infectious diseases and lifestyle-related diseases. The aim of the present article is to expand the application of ultrasensitive ELISAs in the medical and biological fields.
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Affiliation(s)
- Naoko Tsurusawa
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Jyunhao Chang
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Mayuri Namba
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Daiki Makioka
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Sou Yamura
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Kanako Iha
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Yuta Kyosei
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Satoshi Watabe
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan;
| | - Teruki Yoshimura
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu 061-0293, Hokkaido, Japan;
| | - Etsuro Ito
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan;
- Graduate Institute of Medicine, School of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
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