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Article: Mutational basis of serum cross-neutralization profiles elicited by infection or vaccination with SARS-CoV-2 variants.

Wagh, Kshitij / Shen, Xiaoying / Theiler, James / Girard, Bethany / Marshall, Jean-Claude / Montefiori, David C / Korber, Bette

bioRxiv : the preprint server for biology

2023

Abstract: A series of SARS-CoV-2 variants emerged during the pandemic under selection for neutralization resistance. Convalescent and vaccinated sera show consistently different cross-neutralization profiles depending on infecting or vaccine variants. To ... ...

Abstract	A series of SARS-CoV-2 variants emerged during the pandemic under selection for neutralization resistance. Convalescent and vaccinated sera show consistently different cross-neutralization profiles depending on infecting or vaccine variants. To understand the basis of this heterogeneity, we modeled serum cross-neutralization titers for 165 sera after infection or vaccination with historically prominent lineages tested against 18 variant pseudoviruses. Cross-neutralization profiles were well captured by models incorporating autologous neutralizing titers and combinations of specific shared and differing mutations between the infecting/vaccine variants and pseudoviruses. Infecting/vaccine variant-specific models identified mutations that significantly impacted cross-neutralization and quantified their relative contributions. Unified models that explained cross-neutralization profiles across all infecting and vaccine variants provided accurate predictions of holdout neutralization data comprising untested variants as infecting or vaccine variants, and as test pseudoviruses. Finally, comparative modeling of 2-dose versus 3-dose mRNA-1273 vaccine data revealed that the third dose overcame key resistance mutations to improve neutralization breadth. Highlights: Modeled SARS-CoV-2 cross-neutralization using mutations at key sitesIdentified resistance mutations and quantified relative impactAccurately predicted holdout variant and convalescent/vaccine sera neutralizationShowed that the third dose of mRNA-1273 vaccination overcomes resistance mutations.
Language	English
Publishing date	2023-08-14
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.13.553144
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Article ; Online: Neutralization of Omicron Subvariant BA.2.75 after Bivalent Vaccination.

Chalkias, Spyros / Feng, Jing / Chen, Xing / Zhou, Honghong / Marshall, Jean-Claude / Girard, Bethany / Tomassini, Joanne E / Kuter, Barbara J / Montefiori, David C / Das, Rituparna

The New England journal of medicine

2022 Volume 387, Issue 23, Page(s) 2194–2196

Language	English
Publishing date	2022-11-23
Publishing country	United States
Document type	Letter
ZDB-ID	207154-x
ISSN	1533-4406 ; 0028-4793
ISSN (online)	1533-4406
ISSN	0028-4793
DOI	10.1056/NEJMc2212772
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Article ; Online: Mutational basis of serum cross-neutralization profiles elicited by infection or vaccination with SARS-CoV-2 variants

Wagh, Kshitij / Shen, Xiaoying / Theiler, James / Girard, Bethany / Marshall, Jean-Claude / Montefiori, David / Korber, Bette

bioRxiv

Abstract	A series of SARS-CoV-2 variants emerged during the pandemic under selection for neutralization resistance. Convalescent and vaccinated sera show consistently different cross-neutralization profiles depending on infecting or vaccine variants. To understand the basis of this heterogeneity, we modeled serum cross-neutralization titers for 165 sera after infection or vaccination with historically prominent lineages tested against 18 variant pseudoviruses. Cross-neutralization profiles were well captured by models incorporating autologous neutralizing titers and combinations of specific shared and differing mutations between the infecting/vaccine variants and pseudoviruses. Infecting/vaccine variant-specific models identified mutations that significantly impacted cross-neutralization and quantified their relative contributions. Unified models that explained cross-neutralization profiles across all infecting and vaccine variants provided accurate predictions of holdout neutralization data comprising untested variants as infecting or vaccine variants, and as test pseudoviruses. Finally, comparative modeling of 2-dose versus 3-dose mRNA-1273 vaccine data revealed that the third dose overcame key resistance mutations to improve neutralization breadth.
Keywords	covid19
Language	English
Publishing date	2023-08-14
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.08.13.553144
Database	COVID19

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Article ; Online: Current challenges and opportunities for pharmacogenomics: perspective of the Industry Pharmacogenomics Working Group (I-PWG).

Bienfait, Karina / Chhibber, Aparna / Marshall, Jean-Claude / Armstrong, Martin / Cox, Charles / Shaw, Peter M / Paulding, Charles

Human genetics

2021 Volume 141, Issue 6, Page(s) 1165–1173

Abstract: Pharmaceutical companies have increasingly utilized genomic data for the selection of drug targets and the development of precision medicine approaches. Most major pharmaceutical companies routinely collect DNA from clinical trial participants and ... ...

Abstract	Pharmaceutical companies have increasingly utilized genomic data for the selection of drug targets and the development of precision medicine approaches. Most major pharmaceutical companies routinely collect DNA from clinical trial participants and conduct pharmacogenomic (PGx) studies. However, the implementation of PGx studies during clinical development presents a number of challenges. These challenges include adapting to a constantly changing global regulatory environment, challenges in study design and clinical implementation, and the increasing concerns over patient privacy. Advances in the field of genomics are also providing new opportunities for pharmaceutical companies, including the availability of large genomic databases linked to patient health information, the growing use of polygenic risk scores, and the direct sequencing of clinical trial participants. The Industry Pharmacogenomics Working Group (I-PWG) is an association of pharmaceutical companies actively working in the field of pharmacogenomics. This I-PWG perspective will provide an overview of the steps pharmaceutical companies are taking to address each of these challenges, and the approaches being taken to capitalize on emerging scientific opportunities.
MeSH term(s)	DNA ; Genomics ; Humans ; Pharmaceutical Preparations ; Pharmacogenetics ; Precision Medicine
Chemical Substances	Pharmaceutical Preparations ; DNA (9007-49-2)
Language	English
Publishing date	2021-06-03
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	223009-4
ISSN	1432-1203 ; 0340-6717
ISSN (online)	1432-1203
ISSN	0340-6717
DOI	10.1007/s00439-021-02282-3
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Article ; Online: Neutralization of SARS-CoV-2 Omicron BA.2.75 after mRNA-1273 Vaccination.

Shen, Xiaoying / Chalkias, Spyros / Feng, Jing / Chen, Xing / Zhou, Honghong / Marshall, Jean-Claude / Girard, Bethany / Tomassini, Joanne E / Aunins, Anne / Das, Rituparna / Montefiori, David C

The New England journal of medicine

2022 Volume 387, Issue 13, Page(s) 1234–1236

MeSH term(s)	2019-nCoV Vaccine mRNA-1273/immunology ; 2019-nCoV Vaccine mRNA-1273/therapeutic use ; Antibodies, Neutralizing/therapeutic use ; Antibodies, Viral ; COVID-19/immunology ; COVID-19/prevention & control ; COVID-19/virology ; Humans ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus ; Vaccination
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; 2019-nCoV Vaccine mRNA-1273 (EPK39PL4R4)
Language	English
Publishing date	2022-09-09
Publishing country	United States
Document type	Letter
ZDB-ID	207154-x
ISSN	1533-4406 ; 0028-4793
ISSN (online)	1533-4406
ISSN	0028-4793
DOI	10.1056/NEJMc2210648
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Article ; Online: Bioanalysis of adeno-associated virus gene therapy therapeutics: regulatory expectations.

Gorovits, Boris / Marshall, Jean-Claude / Smith, Justin / Whiteley, Laurence O / Neubert, Hendrik

Bioanalysis

2019 Volume 11, Issue 21, Page(s) 2011–2024

Abstract: The number of gene therapy (GTx) modality therapies in development has grown significantly in the last few years. Adeno-associated virus (AAV)-based delivery approach has become most prevalent among other virus-based GTx vectors. Several regulatory ... ...

Abstract	The number of gene therapy (GTx) modality therapies in development has grown significantly in the last few years. Adeno-associated virus (AAV)-based delivery approach has become most prevalent among other virus-based GTx vectors. Several regulatory guidelines provide the industry with general considerations related to AAV GTx development including discussion and recommendations related to highly diverse bioanalytical support of the AAV-based therapeutics. This includes assessment of pre- and post-treatment immunity, evaluation of post-treatment viral shedding and infectivity, as well as detection of transgene protein expression. An overview of the current regulatory recommendations as found in currently active and published draft US FDA and EMA guidance or guideline documents is presented herein.
MeSH term(s)	Animals ; Dependovirus/genetics ; Genetic Therapy/adverse effects ; Genetic Therapy/legislation & jurisprudence ; Genome, Viral/genetics ; Humans ; Immunity/genetics ; Social Control, Formal
Language	English
Publishing date	2019-10-25
Publishing country	England
Document type	Journal Article ; Review
ISSN	1757-6199
ISSN (online)	1757-6199
DOI	10.4155/bio-2019-0135
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Article ; Online: Assessment of inter-racial variability in CYP3A4 activity and inducibility among healthy adult males of Caucasian and South Asian ancestries.

van Dyk, Madelé / Marshall, Jean-Claude / Sorich, Michael J / Wood, Linda S / Rowland, Andrew

European journal of clinical pharmacology

2018 Volume 74, Issue 7, Page(s) 913–920

Abstract: Purpose: Cytochrome P450 (CYP) 3A4 is responsible for the metabolism of more than 30% of clinically used drugs. Inherent between subject variability in clearance of CYP3A4 substrates is substantial; by way of example, midazolam clearance varies by > 10- ... ...

Abstract	Purpose: Cytochrome P450 (CYP) 3A4 is responsible for the metabolism of more than 30% of clinically used drugs. Inherent between subject variability in clearance of CYP3A4 substrates is substantial; by way of example, midazolam clearance varies by > 10-fold between individuals before considering the impact of extrinsic factors. Relatively little is known about inter-racial variability in the activity of this enzyme. Methods: This study assessed inter-racial variability in midazolam exposure in a cohort (n = 30) of CYP3A genotyped, age-matched healthy males of Caucasian and South Asian ancestries. Midazolam exposure was assessed at baseline, following 7 days of rifampicin and following 3 days of clarithromycin. Results: The geometric mean baseline midazolam area under the plasma concentration curve (AUC Conclusions: Significantly higher midazolam clearance was observed in healthy age-matched males of South Asian compared to Caucasian ancestry that was not explained by differences in the frequency of CYP3A genotypes.
MeSH term(s)	Adult ; Area Under Curve ; Asian Continental Ancestry Group/genetics ; Clarithromycin/blood ; Clarithromycin/pharmacokinetics ; Clarithromycin/pharmacology ; Continental Population Groups ; Cytochrome P-450 CYP3A/genetics ; Cytochrome P-450 CYP3A/metabolism ; Cytochrome P-450 CYP3A Inducers/blood ; Cytochrome P-450 CYP3A Inducers/pharmacokinetics ; Cytochrome P-450 CYP3A Inducers/pharmacology ; Cytochrome P-450 CYP3A Inhibitors/blood ; Cytochrome P-450 CYP3A Inhibitors/pharmacokinetics ; Cytochrome P-450 CYP3A Inhibitors/pharmacology ; Enzyme Induction ; European Continental Ancestry Group/genetics ; Genotype ; Humans ; Male ; Midazolam/blood ; Midazolam/pharmacokinetics ; Rifampin/blood ; Rifampin/pharmacokinetics ; Rifampin/pharmacology ; Young Adult
Chemical Substances	Cytochrome P-450 CYP3A Inducers ; Cytochrome P-450 CYP3A Inhibitors ; Cytochrome P-450 CYP3A (EC 1.14.14.1) ; CYP3A4 protein, human (EC 1.14.14.55) ; Clarithromycin (H1250JIK0A) ; Midazolam (R60L0SM5BC) ; Rifampin (VJT6J7R4TR)
Language	English
Publishing date	2018-03-23
Publishing country	Germany
Document type	Clinical Trial ; Journal Article
ZDB-ID	121960-1
ISSN	1432-1041 ; 0031-6970
ISSN (online)	1432-1041
ISSN	0031-6970
DOI	10.1007/s00228-018-2450-4
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Article ; Online: Use of Physiologically Based Pharmacokinetic Modeling to Identify Physiological and Molecular Characteristics Driving Variability in Axitinib Exposure: A Fresh Approach to Precision Dosing in Oncology.

Sorich, Michael J / Mutlib, Fayzah / van Dyk, Madelé / Hopkins, Ashley M / Polasek, Thomas M / Marshall, Jean-Claude / Rodrigues, A David / Rowland, Andrew

Journal of clinical pharmacology

2019 Volume 59, Issue 6, Page(s) 872–879

Abstract: Axitinib is a second-generation small-molecule vascular endothelial growth factor receptor inhibitor. An axitinib steady-state area under the plasma concentration-time curve ( ... ...

Abstract	Axitinib is a second-generation small-molecule vascular endothelial growth factor receptor inhibitor. An axitinib steady-state area under the plasma concentration-time curve (AUC
MeSH term(s)	Albumins/metabolism ; Axitinib/pharmacokinetics ; Biological Variation, Population/drug effects ; Biomarkers ; Biomarkers, Pharmacological ; Cytochrome P-450 CYP3A/metabolism ; Drug Dosage Calculations ; Humans ; Linear Models ; Models, Biological ; Neoplasms/drug therapy ; Receptors, Vascular Endothelial Growth Factor/antagonists & inhibitors
Chemical Substances	Albumins ; Biomarkers ; Biomarkers, Pharmacological ; Axitinib (C9LVQ0YUXG) ; Cytochrome P-450 CYP3A (EC 1.14.14.1) ; Receptors, Vascular Endothelial Growth Factor (EC 2.7.10.1)
Language	English
Publishing date	2019-01-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	188980-1
ISSN	1552-4604 ; 0091-2700 ; 0021-9754
ISSN (online)	1552-4604
ISSN	0091-2700 ; 0021-9754
DOI	10.1002/jcph.1377
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Article ; Online: Meta-Analysis of Noncompartmental Pharmacokinetic Parameters of Ertugliflozin to Evaluate Dose Proportionality and UGT1A9 Polymorphism Effect on Exposure.

Marshall, Jean-Claude / Liang, Yali / Sahasrabudhe, Vaishali / Tensfeldt, Thomas / Fediuk, Daryl J / Zhou, Susan / Krishna, Rajesh / Dawra, Vikas Kumar / Wood, Linda S / Sweeney, Kevin

Journal of clinical pharmacology

2021 Volume 61, Issue 9, Page(s) 1220–1231

Abstract: Ertugliflozin, a sodium-glucose cotransporter 2 inhibitor, is primarily metabolized via glucuronidation by the uridine 5'-diphospho-glucuronosyltransferase (UGT) isoform UGT1A9. This noncompartmental meta-analysis of ertugliflozin pharmacokinetics ... ...

Abstract	Ertugliflozin, a sodium-glucose cotransporter 2 inhibitor, is primarily metabolized via glucuronidation by the uridine 5'-diphospho-glucuronosyltransferase (UGT) isoform UGT1A9. This noncompartmental meta-analysis of ertugliflozin pharmacokinetics evaluated the relationship between ertugliflozin exposure and dose, and the effect of UGT1A9 genotype on ertugliflozin exposure. Pharmacokinetic data from 25 phase 1 studies were pooled. Structural models for dose proportionality described the relationship between ertugliflozin area under the plasma concentration-time curve (AUC) or maximum observed plasma concentration (C
MeSH term(s)	Area Under Curve ; Bridged Bicyclo Compounds, Heterocyclic/administration & dosage ; Bridged Bicyclo Compounds, Heterocyclic/pharmacokinetics ; Clinical Trials, Phase I as Topic ; Dose-Response Relationship, Drug ; Genotype ; Glucuronosyltransferase/genetics ; Humans ; Metabolic Clearance Rate ; Models, Biological ; Polymorphism, Genetic ; Sodium-Glucose Transporter 2 Inhibitors/administration & dosage ; Sodium-Glucose Transporter 2 Inhibitors/pharmacokinetics ; UDP-Glucuronosyltransferase 1A9/genetics
Chemical Substances	Bridged Bicyclo Compounds, Heterocyclic ; Sodium-Glucose Transporter 2 Inhibitors ; ertugliflozin (6C282481IP) ; Glucuronosyltransferase (EC 2.4.1.17) ; UDP-Glucuronosyltransferase 1A9 (EC 2.4.1.17)
Language	English
Publishing date	2021-06-19
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't
ZDB-ID	188980-1
ISSN	1552-4604 ; 0091-2700 ; 0021-9754
ISSN (online)	1552-4604
ISSN	0091-2700 ; 0021-9754
DOI	10.1002/jcph.1866
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Article ; Online: Identification of the caffeine to trimethyluric acid ratio as a dietary biomarker to characterise variability in cytochrome P450 3A activity.

van Dyk, Madelé / Miners, John O / Marshall, Jean-Claude / Wood, Linda S / Hopkins, Ashley / Sorich, Michael J / Rowland, Andrew

European journal of clinical pharmacology

2019 Volume 75, Issue 9, Page(s) 1211–1218

Abstract: Purpose: Cytochrome P450 (CYP) 3A plays an important role in the metabolism of many clinically used drugs and exhibits substantial between-subject variability (BSV) in activity. Current methods to assess variability in CYP3A activity have limitations ... ...

Abstract	Purpose: Cytochrome P450 (CYP) 3A plays an important role in the metabolism of many clinically used drugs and exhibits substantial between-subject variability (BSV) in activity. Current methods to assess variability in CYP3A activity have limitations and there remains a need for a minimally invasive clinically translatable strategy to define CYP3A activity. The purpose of this study was to evaluate the potential for a caffeine metabolic ratio to describe variability in CYP3A activity. Methods: The metabolic ratio 1,3,7-trimethyluric acid (TMU) to caffeine was evaluated as a biomarker to describe variability in CYP3A activity in a cohort (n = 28) of healthy 21 to 35-year-old males. Midazolam, caffeine, and TMU concentrations were assessed at baseline and following dosing of rifampicin (300 mg daily) for 7 days. Results: At baseline, correlation coefficients for the relationship between apparent oral midazolam clearance (CL/F) with caffeine/TMU ratio measured at 3, 4, and 6 h post dose were 0.82, 0.79, and 0.65, respectively. The strength of correlations was retained post rifampicin dosing; 0.72, 0.87, and 0.82 for the ratios at 3, 4, and 6 h, respectively. Weaker correlations were observed between the change in midazolam CL/F and change in caffeine/TMU ratio post/pre-rifampicin dosing. Conclusion: BSV in CYP3A activity was well described by caffeine/TMU ratios pre- and post-induction. The caffeine/TMU ratio may be a convenient tool to assess BSV in CYP3A activity, but assessment of caffeine/TMU ratio alone is unlikely to account for all sources of variability in CYP3A activity.
MeSH term(s)	Adult ; Biomarkers/blood ; Caffeine/blood ; Caffeine/pharmacokinetics ; Continental Population Groups/genetics ; Cytochrome P-450 CYP3A/genetics ; Cytochrome P-450 CYP3A/metabolism ; Cytochrome P-450 CYP3A Inducers/blood ; Cytochrome P-450 CYP3A Inducers/pharmacokinetics ; Diet ; Genotype ; Humans ; Male ; Midazolam/blood ; Midazolam/pharmacokinetics ; Phenotype ; Rifampin/blood ; Rifampin/pharmacokinetics ; Uric Acid/analogs & derivatives ; Uric Acid/blood ; Young Adult
Chemical Substances	Biomarkers ; Cytochrome P-450 CYP3A Inducers ; Uric Acid (268B43MJ25) ; Caffeine (3G6A5W338E) ; 1,3,7-trimethyluric acid (5415-44-1) ; CYP3A protein, human (EC 1.14.14.1) ; Cytochrome P-450 CYP3A (EC 1.14.14.1) ; Midazolam (R60L0SM5BC) ; Rifampin (VJT6J7R4TR)
Language	English
Publishing date	2019-05-23
Publishing country	Germany
Document type	Clinical Trial ; Journal Article
ZDB-ID	121960-1
ISSN	1432-1041 ; 0031-6970
ISSN (online)	1432-1041
ISSN	0031-6970
DOI	10.1007/s00228-019-02682-5
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