1
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Zhang C, McIntosh KD, Sienkiewicz N, Stelzer EA, Graham JL, Lu J. qPCR-based phytoplankton abundance and chlorophyll a: A multi-year study in twelve large freshwater rivers across the United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:175067. [PMID: 39111421 DOI: 10.1016/j.scitotenv.2024.175067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 07/24/2024] [Accepted: 07/24/2024] [Indexed: 09/21/2024]
Abstract
Phytoplankton overgrowth, which characterizes the eutrophication or trophic status of surface water bodies, threatens ecosystems and public health. Quantitative polymerase chain reaction (qPCR) is promising for assessing the abundance and community composition of phytoplankton. However, applications of qPCR to indicate eutrophication and trophic status, especially in lotic systems, have yet to be comprehensively evaluated. For the first time, this study correlates qPCR-based phytoplankton abundance with chlorophyll a (the most widely used indicator of eutrophication and trophic status) in multiple freshwater rivers. From early summer to late fall in 2017, 2018, and 2019, we evaluated phytoplankton, chlorophyll a, pheophytin a, and the Trophic Level Index (TLI) in twelve large freshwater rivers in three regions (western, midcontinent, and eastern) in the United States. Chlorophyll a concentration had positive allometric correlations with qPCR-based phytoplankton abundance (adjusted R2 = 0.5437, p-value < 0.001), pheophytin a concentration (adjusted R2 = 0.3378, p-value <0.001), and TLI (adjusted R2 = 0.4789, p-value < 0.001). Thus, a greater phytoplankton abundance suggests a higher trophic status. This work also presents the numerical values of qPCR-based phytoplankton abundance defining the boundaries among trophic statuses (e.g., oligotrophic, mesotrophic, and eutrophic) of freshwater rivers. The sampling sites in the midcontinent rivers were more eutrophic because they had significantly higher chlorophyll a concentrations, pheophytin a concentrations, and TLI values than the sites in the western and eastern rivers. The higher phytoplankton abundance at the midcontinent sites confirmed their higher trophic status. By linking qPCR-based phytoplankton abundance to chlorophyll a, this study demonstrates that qPCR is a promising avenue to investigate the population dynamics of phytoplankton and the trophic status (or eutrophication) of freshwater rivers.
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Affiliation(s)
- Chiqian Zhang
- Civil Engineering Program, College of Engineering & Computer Science, Arkansas State University, AR 72467, United States
| | - Kyle D McIntosh
- Oak Ridge Institute for Science and Education at the United States Environmental Protection Agency's Office of Research and Development, Oak Ridge, TN 37830, United States
| | - Nathan Sienkiewicz
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, United States
| | - Erin A Stelzer
- U.S. Geological Survey, Columbus, OH 43229, United States
| | | | - Jingrang Lu
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, United States.
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2
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Xu R, Njumbe Ediage E, Verhaeghe T, Snoeys J, Dillen L. Therapeutic siRNA Loaded to RISC as Single and Double Strands Requires an Appropriate Quantitative Assay for RISC PK Assessment. Nucleic Acid Ther 2024; 34:199-210. [PMID: 38638105 DOI: 10.1089/nat.2023.0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
In recent years, therapeutic siRNA projects are booming in the biotech and pharmaceutical industries. As these drugs act by silencing the target gene expression, a critical step is the binding of antisense strands of siRNA to RNA-induced silencing complex (RISC) and then degrading their target mRNA. However, data that we recently obtained suggest that double-stranded siRNA can also load to RISC. This brings a new understanding of the mechanism of RISC loading which may have a potential impact on how quantification of RISC loaded siRNA should be performed. By combining RNA immune precipitation and probe-based hybridization LC-fluorescence approach, we have developed a novel assay that can accurately quantify the RISC-bound antisense strand, irrespective of which form (double-stranded or single-stranded) is loaded on RISC. In addition, this novel assay can discriminate between the 5'-phosphorylated antisense (5'p-AS) and the nonphosphorylated forms, therefore specifically quantifying the RISC bound 5'p-AS. In comparison, stem-loop qPCR assay does not provide discrimination and accurate quantification when the oligonucleotide analyte exists as a mixture of double and single-stranded forms. Taking together, RISC loading assay with probe-hybridization LC-fluorescence technique would be a more accurate and specific quantitative approach for RISC-associated pharmacokinetic assessment.
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Affiliation(s)
- Rui Xu
- Bioanalytical Discovery & Development Sciences (BDDS), Preclinical Sciences & Translational Safety (PSTS), Research & Development (R&D), Janssen Pharmaceutica NV, A Johnson & Johnson Company, Beerse, Belgium
| | - Emmanuel Njumbe Ediage
- Bioanalytical Discovery & Development Sciences (BDDS), Preclinical Sciences & Translational Safety (PSTS), Research & Development (R&D), Janssen Pharmaceutica NV, A Johnson & Johnson Company, Beerse, Belgium
| | - Tom Verhaeghe
- Bioanalytical Discovery & Development Sciences (BDDS), Preclinical Sciences & Translational Safety (PSTS), Research & Development (R&D), Janssen Pharmaceutica NV, A Johnson & Johnson Company, Beerse, Belgium
| | - Jan Snoeys
- Translational Pharmacokinetics/ Pharmacodynamics & Investigative Toxicology (TPPIT), Preclinical Sciences & Translational Safety (PSTS), Research & Development (R&D), Janssen Pharmaceutica NV, A Johnson & Johnson Company, Beerse, Belgium
| | - Lieve Dillen
- Bioanalytical Discovery & Development Sciences (BDDS), Preclinical Sciences & Translational Safety (PSTS), Research & Development (R&D), Janssen Pharmaceutica NV, A Johnson & Johnson Company, Beerse, Belgium
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3
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Agrawal K, Calliste LK, Ji S, Xu S, Ayers SA, Jian W. Comparison of multiple bioanalytical assay platforms for the quantitation of siRNA therapeutics. Bioanalysis 2024; 16:651-667. [PMID: 39254503 PMCID: PMC11389733 DOI: 10.1080/17576180.2024.2350266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/29/2024] [Indexed: 09/11/2024] Open
Abstract
Aim: Oligonucleotide therapeutics can be quantified using various bioanalytical methods, and these methods have been compared extensively. However, few comparisons exist where the same analyte is evaluated by multiple assay platforms.Materials & methods: Hybrid LC-MS, SPE-LC-MS, HELISA and SL-RT-qPCR methods were developed for an siRNA analyte, and samples from a pharmacokinetic study were analyzed by all four methods.Results: All assay platforms provided comparable data, though higher concentrations were observed using the non-LC-MS assays. Hybrid LC-MS and SL-RT-qPCR were the most sensitive methodologies, and SL-RT-qPCR and HELISA demonstrated the highest throughput.Conclusion: Each assay platform is suitable for oligonucleotide bioanalysis, and the ultimate choice of methodology will depend on the prioritization of needs such as sensitivity, specificity and throughput.
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Affiliation(s)
- Karan Agrawal
- Bioanalysis Discovery & Development Sciences, Janssen Research & Development, LLC, Spring House, PA 19477, USA
| | - Laurelle K Calliste
- Bioanalysis Discovery & Development Sciences, Janssen Research & Development, LLC, Spring House, PA 19477, USA
| | - Shaofei Ji
- Translational PK/PD & Investigative Toxicology, Janssen Research & Development, LLC, Spring House, PA 19477, USA
| | - Shengsheng Xu
- Bioanalysis Discovery & Development Sciences, Janssen Research & Development, LLC, Spring House, PA 19477, USA
| | - Stephen A Ayers
- Bioanalysis Discovery & Development Sciences, Janssen Research & Development, LLC, Spring House, PA 19477, USA
| | - Wenying Jian
- Bioanalysis Discovery & Development Sciences, Janssen Research & Development, LLC, Spring House, PA 19477, USA
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4
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Shiga M, Asari M, Takahashi Y, Isozaki S, Hoshina C, Mori K, Namba R, Okuda K, Shimizu K. DNA methylation-based age estimation and quantification of the degradation levels of bisulfite-converted DNA. Leg Med (Tokyo) 2024; 67:102336. [PMID: 37923589 DOI: 10.1016/j.legalmed.2023.102336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023]
Abstract
DNA methylation modifications are known to influence epigenetic phenomena and have been a focus of forensic science research for some time. Degraded DNA after bisulfite treatment is widely used in DNA methylation analysis. In this study, we analyzed methylation levels at 12 CpG sites of four selected genomic regions by pyrosequencing after bisulfite treatment. DNA was extracted from buccal swab samples collected from 102 Japanese individuals who were 21-77 years old. We also developed a simple method to quantify the degradation levels of bisulfite-converted DNA by real-time PCR, and evaluated the effect of DNA degradation on age estimation. We found that the methylation levels and chronological ages were highly correlated in the four selected regions, and the mean absolute deviation (MAD) between chronological and estimated ages was low at 3.88 years. These results indicated that pyrosequencing analysis at the 12 CpGs was useful for age estimation in the Japanese population. To develop a sensitive quantification method, we analyzed the amplification efficiency of short and long fragments from 10 regions by real-time PCR. The amplification efficiency was highest for CCDC102B, and the degradation levels of bisulfite-converted DNA for the 102 samples were categorized as moderately or heavily degraded. For the younger age groups (20-49 years), the MADs were lower for moderately degraded DNA than they were for heavily degraded DNA. This finding indicates that degradation levels affected the accuracy of age estimation in most of the samples; the exception was the samples from the 50-77 years age group.
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Affiliation(s)
- Mihiro Shiga
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; Department of Orthopaedic Surgery, Keiyukai Medical Foundation Yoshida Hospital, Asahikawa 070-0054, Japan
| | - Masaru Asari
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan.
| | - Yuta Takahashi
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Shotaro Isozaki
- Department of Forensic Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Chisato Hoshina
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Kanae Mori
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Ryo Namba
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Katsuhiro Okuda
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Keiko Shimizu
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
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5
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Turski MK, Albertolle ME. Utilizing droplet digital polymerase chain reaction for siRNA quantitation in rodent plasma and tissue via stem-loop reverse transcription. Bioanalysis 2024; 16:375-388. [PMID: 38380639 DOI: 10.4155/bio-2023-0228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Background: siRNA is a promising therapeutic modality highlighted by several US FDA approvals since 2018, with many more oligonucleotide assets in clinical development. To support siRNA discovery and development, robust and sensitive quantitative platforms for bioanalysis must be established to assess pharmacokinetic/pharmacodynamic relationships and toxicology. Droplet digital PCR offers improved sensitivity and throughput, as well as reduced susceptibility to matrix effects, compared with other analytical platforms. Methodology: The authors developed a stem-loop reverse transcription droplet digital PCR method to measure siRNA in mouse plasma and liver extract using bioanalytical method qualification guidelines. Conclusion: This newly developed assay has been demonstrated to be a superior alternative to other platforms, with the added benefit of greater sensitivity, with dynamic range from 390 to 400,000 copies/reaction and readiness for FDA investigational new drug-enabling applications.
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Affiliation(s)
- Megan K Turski
- Global Drug Metabolism. Pharmacokinetics & Modeling, Takeda Development Center Americas, San Diego, CA, USA
| | - Matthew E Albertolle
- Global Drug Metabolism. Pharmacokinetics & Modeling, Takeda Development Center Americas, San Diego, CA, USA
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6
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Hays A, Wissel M, Colletti K, Soon R, Azadeh M, Smith J, Doddareddy R, Chalfant M, Adamowicz W, Ramaswamy SS, Dholakiya SL, Guelman S, Gullick B, Durham J, Rennier K, Nagilla P, Muruganandham A, Diaz M, Tierney C, John K, Valentine J, Lockman T, Liu HY, Moritz B, Ouedraogo JP, Piche MS, Smet M, Murphy J, Koenig K, Zybura A, Vyhlidal C, Mercier J, Jani N, Kubista M, Birch D, Morse K, Johansson O. Recommendations for Method Development and Validation of qPCR and dPCR Assays in Support of Cell and Gene Therapy Drug Development. AAPS J 2024; 26:24. [PMID: 38316745 DOI: 10.1208/s12248-023-00880-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/06/2023] [Indexed: 02/07/2024] Open
Abstract
The emerging use of qPCR and dPCR in regulated bioanalysis and absence of regulatory guidance on assay validations for these platforms has resulted in discussions on lack of harmonization on assay design and appropriate acceptance criteria for these assays. Both qPCR and dPCR are extensively used to answer bioanalytical questions for novel modalities such as cell and gene therapies. Following cross-industry conversations on the lack of information and guidelines for these assays, an American Association of Pharmaceutical Scientists working group was formed to address these gaps by bringing together 37 industry experts from 24 organizations to discuss best practices to gain a better understanding in the industry and facilitate filings to health authorities. Herein, this team provides considerations on assay design, development, and validation testing for PCR assays that are used in cell and gene therapies including (1) biodistribution; (2) transgene expression; (3) viral shedding; (4) and persistence or cellular kinetics of cell therapies.
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Affiliation(s)
- Amanda Hays
- BioAgilytix Laboratories, Durham, North Carolina, USA.
| | - Mark Wissel
- Eurofins Viracor BioPharma Services, Inc., Lenexa, Kansas, USA
| | | | - Russell Soon
- BioMarin Pharmaceutical Inc., Novato, California, USA
| | - Mitra Azadeh
- Ultragenyx Pharmaceutical Inc., Novato, Calfornia, USA
| | | | | | | | - Wendy Adamowicz
- PPD Clinical Research, Thermo Fisher Scientific, Richmond, Virginia, USA
| | | | | | | | - Bryan Gullick
- BioAgilytix Laboratories, Durham, North Carolina, USA
| | | | | | - Pruthvi Nagilla
- Asher Biotherapeutics, Inc., South San Francisco, California, USA
| | | | - Manisha Diaz
- Eurofins Viracor BioPharma Services, Inc., Lenexa, Kansas, USA
| | | | | | | | - Timothy Lockman
- PPD Clinical Research, Thermo Fisher Scientific, Richmond, Virginia, USA
| | - Hsing-Yin Liu
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | | | | | | | | | - Jacqueline Murphy
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Kaylyn Koenig
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
| | - Agnes Zybura
- Labcorp Drug Development, Greenfield, Indiana, USA
| | - Carrie Vyhlidal
- KCAS Bioanalytical and Biomarker Services, Shawnee, Kansas, USA
| | | | - Niketa Jani
- BioAgilytix Laboratories, Boston, Massachusetts, USA
| | - Mikael Kubista
- Institute of Biotechnology Czech Academy of Sciences, Prague, Czech Republic
| | - Donald Birch
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
| | - Karlin Morse
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
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7
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Gokemeijer J, Balasubramanian N, Ogasawara K, Grudzinska-Goebel J, Upreti VV, Mody H, Kasar S, Vepachedu VR, Xu W, Gupta S, Tarcsa E, Dodge R, Herr K, Yang TY, Tourdot S, Jawa V. An IQ Consortium Perspective on Best Practices for Bioanalytical and Immunogenicity Assessment Aspects of CAR-T and TCR-T Cellular Therapies Development. Clin Pharmacol Ther 2024; 115:188-200. [PMID: 37983584 DOI: 10.1002/cpt.3111] [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: 08/07/2023] [Accepted: 11/05/2023] [Indexed: 11/22/2023]
Abstract
CAR-T therapies have shown remarkable efficacy against hematological malignancies in the clinic over the last decade and new studies indicate that progress is being made to use these novel therapies to target solid tumors as well as treat autoimmune disease. Innovation in the field, including TCR-T, allogeneic or "off the shelf" CAR-T, and autoantigen/armored CAR-Ts are likely to increase the efficacy and applications of these therapies. The unique aspects of these cell-based therapeutics; patient-derived cells, intracellular expression, in vivo expansion, and phenotypic changes provide unique bioanalytical challenges to develop pharmacokinetic and immunogenicity assessments. The International Consortium for Innovation and Quality in Pharmaceutical Development (IQ) Translational and ADME Sciences Leadership Group (TALG) has brought together a group of industry experts to discuss and consider these challenges. In this white paper, we present the IQ consortium perspective on the best practices and considerations for bioanalytical and immunogenicity aspects toward the optimal development of CAR-T and TCR-T cell therapies.
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Affiliation(s)
- Jochem Gokemeijer
- Discovery Biotherapeutics, Bristol Myers Squibb, Cambridge, Massachusetts, USA
| | - Nanda Balasubramanian
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Ken Ogasawara
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | | | - Vijay V Upreti
- Clinical Pharmacology, Modeling & Simulation, Amgen, Inc., South San Francisco, California, USA
| | - Hardik Mody
- Clinical Pharmacology, Genentech Inc., South San Francisco, California, USA
| | - Siddha Kasar
- Oncology Precision & Translational Medicine, Takeda Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Venkata R Vepachedu
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Weifeng Xu
- Preclinical Development, Bioanalytical, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Swati Gupta
- Development Biological Sciences, Immunology, AbbVie, Irvine, California, USA
| | - Edit Tarcsa
- Abbvie Bioresearch Center, Worcester, Massachusetts, USA
| | - Robert Dodge
- Novartis Institutes for BioMedical Research, One Health Plaza, East Hanover, New Jersey, USA
| | - Kate Herr
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Tong-Yuan Yang
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Sophie Tourdot
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Vibha Jawa
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
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8
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Sun Y, Nakamura T, Ohtsu Y, Kakehi M, Danno N, Shimizu H, Tanaka Y, Serelli-Lee V, Tanaka S, Okayama T, Suda Y, Moriya Y, Hanada T, Saito Y. Development and validation of qPCR methods for nucleic acid biomarkers as a drug development tool: points to consider. Bioanalysis 2023; 15:1069-1081. [PMID: 37584367 DOI: 10.4155/bio-2023-0071] [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] [Indexed: 08/17/2023] Open
Abstract
Nucleic acid (NA) biomarkers play critical roles in drug development. However, the global regulatory guidelines for assessing quantification methods specific to NA biomarkers are limited. The validation of analytical methods is crucial for the use of biomarkers in clinical and post-marketing evaluations of drug efficacy and adverse reactions. Given that quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR) methods are the gold standards for the quantification of NA biomarkers, the Biomarker Analytical Method Validation Study Group in Japan has discussed considerations and made recommendations for the development and validation of qPCR- and RT-qPCR-based analytical methods for endogenous NA biomarkers as drug development tools. This white paper aims to contribute to the global harmonization of NA biomarker assay validation.
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Affiliation(s)
- Yuchen Sun
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kanagawa, 210-9501, Japan
| | - Takahiro Nakamura
- Shin Nippon Biomedical Laboratories, Ltd, Kagoshima, 891-1394, Japan
| | | | - Masaaki Kakehi
- Takeda Pharmaceutical Company, Limited, Kanagawa, 251-8555, Japan
| | - Noriyuki Danno
- CMIC Pharma Science Co., Ltd, Yamanashi, 408-0044, Japan
| | | | - Yoichi Tanaka
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kanagawa, 210-9501, Japan
| | - Victoria Serelli-Lee
- Eli Lilly Japan KK, Hyogo, 651-0086, Japan
- Clinical evaluation sub-committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, Tokyo, 103-0023, Japan
| | - Seiji Tanaka
- ASKA Pharmaceutical Co., Ltd, Kanagawa, 251-8555, Japan
| | | | - Yusuke Suda
- Nippon Shinyaku Co., Ltd, Kyoto, 601-8550, Japan
| | - Yuu Moriya
- Takeda Pharmaceutical Company, Limited, Kanagawa, 251-8555, Japan
| | | | - Yoshiro Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kanagawa, 210-9501, Japan
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9
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Masilamani M, Jawa V, Dai Y, Das R, Park A, Lamba M, Wu F, Zheng X, Lu E, Gleason C, Mack T, Mora J, Surapaneni S. Bioanalytical Methods for Characterization of CAR-T Cellular Kinetics: Comparison of PCR Assays and Matrices. Clin Pharmacol Ther 2023; 114:664-672. [PMID: 37422675 DOI: 10.1002/cpt.2991] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023]
Abstract
Recently, multiple chimeric antigen receptor T-cell (CAR-T)-based therapies have been approved for treating hematological malignancies, targeting CD19 and B-cell maturation antigen. Unlike protein or antibody therapies, CAR-T therapies are "living cell" therapies whose pharmacokinetics are characterized by expansion, distribution, contraction, and persistence. Therefore, this unique modality requires a different approach for quantitation compared with conventional ligand binding assays implemented for most biologics. Cellular (flow cytometry) or molecular assays (polymerase chain reaction (PCR)) can be deployed with each having unique advantages and disadvantages. In this article, we describe the molecular assays utilized: quantitative PCR (qPCR), which was the initial platform used to estimate transgene copy numbers and more recently droplet digital PCR (ddPCR) which quantitates the absolute copy numbers of CAR transgene. The comparability of the two methods in patient samples and of each method across different matrices (isolated CD3+ T-cells or whole blood) was also performed. The results show a good correlation between qPCR and ddPCR for the amplification of same gene in clinical samples from a CAR-T therapy trial. In addition, our studies show that the qPCR-based amplification of transgene levels was well-correlated, independent of DNA sources (either CD3+ T-cells or whole blood). Our results also highlight that ddPCR can be a better platform for monitoring samples at the early phase of CAR-T dosing prior to expansion and during long-term monitoring as they can detect samples with very low copy numbers with high sensitivity, in addition to easier implementation and sample logistics.
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Affiliation(s)
- Madhan Masilamani
- Department of Clinical Pharmacology, Pharmacometrics, Disposition, and Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Vibha Jawa
- Department of Clinical Pharmacology, Pharmacometrics, Disposition, and Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Yanshan Dai
- Department of Clinical Pharmacology, Pharmacometrics, Disposition, and Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Romita Das
- Department of Clinical Pharmacology, Pharmacometrics, Disposition, and Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Alice Park
- Department of Clinical Pharmacology, Pharmacometrics, Disposition, and Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Manisha Lamba
- Department of Clinical Pharmacology, Pharmacometrics, Disposition, and Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Fan Wu
- Department of Clinical Pharmacology, Pharmacometrics, Disposition, and Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Xirong Zheng
- Department of Clinical Pharmacology, Pharmacometrics, Disposition, and Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Edwin Lu
- Global Biometrics and Data Sciences, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Carol Gleason
- Global Biometrics and Data Sciences, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Tim Mack
- Department of Clinical Pharmacology, Pharmacometrics, Disposition, and Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Johanna Mora
- Department of Clinical Pharmacology, Pharmacometrics, Disposition, and Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Sekhar Surapaneni
- Department of Clinical Pharmacology, Pharmacometrics, Disposition, and Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
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10
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Kavita U, Sun K, Braun M, Lembke W, Mody H, Kamerud J, Yang TY, Braun IV, Fang X, Gao W, Gupta S, Hofer M, Liao MZ, Loo L, McBlane F, Menochet K, Stubenrauch KG, Upreti VV, Vigil A, Wiethoff CM, Xia CQ, Zhu X, Jawa V, Chemuturi N. PK/PD and Bioanalytical Considerations of AAV-Based Gene Therapies: an IQ Consortium Industry Position Paper. AAPS J 2023; 25:78. [PMID: 37523051 DOI: 10.1208/s12248-023-00842-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023] Open
Abstract
Interest and efforts to use recombinant adeno-associated viruses (AAV) as gene therapy delivery tools to treat disease have grown exponentially. However, gaps in understanding of the pharmacokinetics/pharmacodynamics (PK/PD) and disposition of this modality exist. This position paper comes from the Novel Modalities Working Group (WG), part of the International Consortium for Innovation and Quality in Pharmaceutical Development (IQ). The pan-industry WG effort focuses on the nonclinical PK and clinical pharmacology aspects of AAV gene therapy and related bioanalytical considerations.Traditional PK concepts are generally not applicable to AAV-based therapies due to the inherent complexity of a transgene-carrying viral vector, and the multiple steps and analytes involved in cell transduction and transgene-derived protein expression. Therefore, we explain PK concepts of biodistribution of AAV-based therapies and place key terminologies related to drug exposure and PD in the proper context. Factors affecting biodistribution are presented in detail, and guidelines are provided to design nonclinical studies to enable a stage-gated progression to Phase 1 testing. The nonclinical and clinical utility of transgene DNA, mRNA, and protein analytes are discussed with bioanalytical strategies to measure these analytes. The pros and cons of qPCR vs. ddPCR technologies for DNA/RNA measurement and qualitative vs. quantitative methods for transgene-derived protein are also presented. Last, best practices and recommendations for use of clinical and nonclinical data to project human dose and response are discussed. Together, the manuscript provides a holistic framework to discuss evolving concepts of PK/PD modeling, bioanalytical technologies, and clinical dose selection in gene therapy.
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Affiliation(s)
- Uma Kavita
- Spark Therapeutics, Inc., Philadelphia, Pennsylvania, 19104, USA.
| | - Kefeng Sun
- Takeda Development Center Americas Inc., 125 Binney St, Cambridge, Massachusetts, 02142, USA.
| | - Manuela Braun
- Bayer AG, Pharmaceuticals R&D, 13342, Berlin, Germany
| | - Wibke Lembke
- Integrated Biologix GmbH, 4051, Basel, Switzerland
| | - Hardik Mody
- Genentech Inc., South San Francisco, California, USA
| | | | - Tong-Yuan Yang
- Janssen R&D LLC., Spring House, Pennsylvania, 19477, USA
| | | | - Xiaodong Fang
- Asklepios BioPharmaceutical, Inc., Research Triangle, North Carolina, 27709, USA
| | - Wei Gao
- EMD Serono Research & Development Institute, Inc., Billerica, Massachusetts, 01821, USA
| | - Swati Gupta
- AbbVie, 2525 Dupont Drive, Irvine, California, 92612, USA
| | - Magdalena Hofer
- Spark Therapeutics, Inc., Philadelphia, Pennsylvania, 19104, USA
| | | | - LiNa Loo
- Vertex Pharmaceuticals Boston, Boston, Massachusetts, 02210, USA
| | | | | | | | | | - Adam Vigil
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, 06877, USA
| | | | - Cindy Q Xia
- ReNAgade Therapeutics, Cambridge, Massachusetts, 02142, USA
| | - Xu Zhu
- AstraZeneca, Waltham, Massachusetts, 02451, USA
| | - Vibha Jawa
- Bristol Myers Squibb, Lawrence Township, New Jersey, 08648, USA
| | - Nagendra Chemuturi
- Takeda Development Center Americas Inc., 125 Binney St, Cambridge, Massachusetts, 02142, USA
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11
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Schröder HM, Niebergall-Roth E, Norrick A, Esterlechner J, Ganss C, Frank MH, Kluth MA. Drug Regulatory-Compliant Validation of a qPCR Assay for Bioanalysis Studies of a Cell Therapy Product with a Special Focus on Matrix Interferences in a Wide Range of Organ Tissues. Cells 2023; 12:1788. [PMID: 37443822 PMCID: PMC10340683 DOI: 10.3390/cells12131788] [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: 05/25/2023] [Revised: 06/23/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Quantitative polymerase chain reaction (qPCR) has emerged as an important bioanalytical method for assessing the pharmacokinetics of human-cell-based medicinal products after xenotransplantation into immunodeficient mice. A particular challenge in bioanalytical qPCR studies is that the different tissues of the host organism can affect amplification efficiency and amplicon detection to varying degrees, and ignoring these matrix effects can easily cause a significant underestimation of the true number of target cells in a sample. Here, we describe the development and drug regulatory-compliant validation of a TaqMan® qPCR assay for the quantification of mesenchymal stromal cells in the range of 125 to 20,000 cells/200 µL lysate via the amplification of a human-specific, highly repetitive α-satellite DNA sequence of the chromosome 17 centromere region HSSATA17. An assessment of matrix effects in 14 different mouse tissues and blood revealed a wide range of spike recovery rates across the different tissue types, from 11 to 174%. Based on these observations, we propose performing systematic spike-and-recovery experiments during assay validation and correcting for the effects of the different tissue matrices on cell quantification in subsequent bioanalytical studies by multiplying the back-calculated cell number by tissue-specific factors derived from the inverse of the validated percent recovery rate.
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Affiliation(s)
| | | | | | | | | | - Markus H. Frank
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
- Transplant Research Program, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia
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12
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Hays A, Durham J, Gullick B, Rudemiller N, Schneider T. Bioanalytical Assay Strategies and Considerations for Measuring Cellular Kinetics. Int J Mol Sci 2022; 24:ijms24010695. [PMID: 36614138 PMCID: PMC9820866 DOI: 10.3390/ijms24010695] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/14/2022] [Accepted: 12/21/2022] [Indexed: 01/04/2023] Open
Abstract
A vast evolution of drug modalities has occurred over the last several decades. Novel modalities such as cell and gene therapies have proven to be efficacious for numerous clinical indications-primarily in rare disease and immune oncology. Because of this success, drug developers are heavily investing in these novel modalities. Given the complexity of these therapeutics, a variety of bioanalytical techniques are employed to fully characterize the pharmacokinetics of these therapies in clinical studies. Industry trends indicate that quantitative PCR (qPCR) and multiparameter flow cytometry are both valuable in determining the pharmacokinetics, i.e. cellular kinetics, of cell therapies. This manuscript will evaluate the pros and cons of both techniques and highlight regulatory guidance on assays for measuring cellular kinetics. Moreover, common considerations when developing these assays will be addressed.
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13
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Development and validation of methods that enable high-quality droplet digital PCR and hematological profiling data from microvolume blood samples. Bioanalysis 2022; 14:1197-1211. [PMID: 36331037 DOI: 10.4155/bio-2022-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aim: Mouse models have been crucial to preclinical studies in the increasingly relevant fields of cell and gene therapy. However, only small quantities of mouse blood can be collected without producing adverse physiological effects that compromise data integrity. Results: To address this limitation, two combined methods were developed to create detailed droplet digital PCR (ddPCR) and hematological profiles using only ∼20 μl of mouse blood. The validation of these methods, which can serve as a foundation for a standardized regulatory pipeline for ddPCR, is discussed. Even when using small amounts of input, this ddPCR protocol is accurate, precise, selective, specific, stable and robust. Conclusion: These techniques enable more frequent sample collection for higher-resolution pharmacokinetic data that meets or exceeds quality standards.
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