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Pu J, Xue C, Huo S, Shen Q, Qu Y, Yang X, An B, Angel TE, Chen Z, Mehl JT, Tang H, Yang E, Sikorski TW, Qu J. Highly Accurate and Robust Absolute Quantification of Target Proteins in Formalin-Fixed Paraffin-Embedded (FFPE) Tissues by LC-MS. Anal Chem 2023; 95:924-934. [PMID: 36534410 PMCID: PMC10581745 DOI: 10.1021/acs.analchem.2c03473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate, absolute liquid chromatography-mass spectrometry (LC-MS)-based quantification of target proteins in formalin-fixed paraffin-embedded (FFPE) tissues would greatly expand sample availability for pharmaceutical/clinical investigations but remains challenging owing to the following issues: (i) efficient/quantitative recovery of target signature peptides from FFPE tissues is essential but an optimal procedure for targeted, absolute quantification is lacking; (ii) most FFPE samples are long-term-stored; severe immunohistochemistry (IHC) signal losses of target proteins during storage were widely reported, while the effect of storage on LC-MS-based methods was unknown; and (iii) the proper strategy to prepare calibration/quality-control samples to ensure accurate targeted protein analysis in FFPE tissues remained elusive. Using targeted quantification of monoclonal antibody (mAb), antigen, and 40 tissue markers in FFPE tissues as a model system, we extensively investigate those issues and develope an LC-MS-based strategy enabling accurate and precise targeted protein quantification in FFPE samples. First, we demonstrated a surfactant cocktail-based procedure (f-SEPOD), providing high/reproducible recovery of target signature peptides from FFPE tissues. Second, a heat-accelerated degradation study within a roughly estimated 5 year storage period recapitulated the loss of protein IHC signals while LC-MS signals of all targets remained constant. This indicates that the storage of FFPE tissues mainly causes decreased immunoreactivity but unlikely chemical degradation of proteins, which strongly suggests that the storage of FFPE tissues does not cause significant quantitative bias for LC-MS-based methods. Third, while a conventional spike-and-extract approach for calibration caused substantial negative biases, a novel approach, using FFPE-treated calibration standards, enabled accurate and precise quantification. With the pipeline, we conducted the first-ever pharmacokinetics measurement of mAb and its target in FFPE tissues, where time courses by FFPE vs fresh tissues showed excellent correlation.
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Affiliation(s)
- Jie Pu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Chao Xue
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Shihan Huo
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Qingqing Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Yang Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Xinxin Yang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Bo An
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Thomas E. Angel
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Zhuo Chen
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - John T. Mehl
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Huaping Tang
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Eric Yang
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Timothy W. Sikorski
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States; Phone: (610) 270-4978
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
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An B, Zhang M, Pu J, Qu Y, Shen S, Zhou S, Ferrari L, Vazvaei F, Qu J. Toward Accurate and Robust Liquid Chromatography–Mass Spectrometry-Based Quantification of Antibody Biotherapeutics in Tissues. Anal Chem 2020; 92:15152-15161. [DOI: 10.1021/acs.analchem.0c03620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Bo An
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Science, Buffalo, New York 14203, United States
- Protein MS, In-vitro/In-vivo Translation, GlaxoSmithKline Pharmaceuticals, Collegeville, Pennsylvania 19426, United States
| | - Ming Zhang
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Science, Buffalo, New York 14203, United States
| | - Jie Pu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Science, Buffalo, New York 14203, United States
| | - Yang Qu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Science, Buffalo, New York 14203, United States
| | - Shichen Shen
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Science, Buffalo, New York 14203, United States
| | - Shaolian Zhou
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel CH-4070, Switzerland
| | - Luca Ferrari
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel CH-4070, Switzerland
| | - Faye Vazvaei
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center New York, Buffalo, New York 10016, United States
| | - Jun Qu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Science, Buffalo, New York 14203, United States
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Chang HP, Kim SJ, Shah DK. Whole-Body Pharmacokinetics of Antibody in Mice Determined using Enzyme-Linked Immunosorbent Assay and Derivation of Tissue Interstitial Concentrations. J Pharm Sci 2020; 110:446-457. [PMID: 32502472 DOI: 10.1016/j.xphs.2020.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/06/2020] [Accepted: 05/20/2020] [Indexed: 12/20/2022]
Abstract
Here we have reported whole-body disposition of wild-type IgG and FcRn non-binding IgG in mice, determined using Enzyme-Linked Immunosorbent Assay (ELISA). The disposition data generated using ELISA are compared with previously published biodistribution data generated using radiolabelled IgG. In addition, we introduce a novel concept of ABCIS values, which are defined as percentage ratios of tissue interstitial and plasma AUC values. These values can help in predicting tissue interstitial concentrations of monoclonal antibodies (mAbs) based on the plasma concentrations. Tissue interstitial concentrations derived from our study are also compared with previously reported values measured using microdialysis or centrifugation method. Lastly, the new set of biodistribution data generated using ELISA are used to refine the PBPK model for mAbs.
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Affiliation(s)
- Hsuan-Ping Chang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Se Jin Kim
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Dhaval K Shah
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, NY, USA.
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An B, Zhang M, Pu J, Shen S, Qu Y, Chen YJ, Huo S, Wang X, Polli JR, Balthasar JP, Herzog D, Ferrari L, Staack RF, Richter WF, Otteneder MB, Benincosa LJ, Zhou S, Vazvaei F, Qu J. High-Throughput, Sensitive LC-MS Quantification of Biotherapeutics and Biomarkers Using Antibody-Free, Peptide-Level, Multiple-Mechanism Enrichment via Strategic Regulation of pH and Ionic and Solvent Strengths. Anal Chem 2019; 91:3475-3483. [DOI: 10.1021/acs.analchem.8b05046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Bo An
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Ming Zhang
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Jie Pu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Shichen Shen
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Yang Qu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Yuan-Ju Chen
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Shihan Huo
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Xue Wang
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Joseph Ryan Polli
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Joseph P. Balthasar
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Denis Herzog
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Luca Ferrari
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Roland F. Staack
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Munich, DE-82377 Penzberg, Germany
| | - Wolfgang F. Richter
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Michael B. Otteneder
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Lisa J. Benincosa
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Shaolian Zhou
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Faye Vazvaei
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center New York, New York, New York 10016, United States
| | - Jun Qu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
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Ocular bioanalysis: challenges and advancements in recent years for these rare matrices. Bioanalysis 2017; 9:1997-2014. [DOI: 10.4155/bio-2017-0175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
There are many ocular diseases still presenting unmet medical needs. Therefore, new ophthalmologic drugs are being developed. Bioanalysis of eye compartments (along with plasma and other tissues) is important to determine exposure of the target organ to the drug and to help interpret local pharmacological or toxic effects. This review article identifies several challenges that occur within ocular bioanalysis. They include sample collection and preparation, analytical issues, sourcing control matrix, data interpretation and regulatory requirements. It summarizes how these challenges have been recently addressed, how research has advanced and which questions remain unanswered. Recommendations are made based on the literature and our practical experience within ocular bioanalysis and future perspectives are discussed.
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