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Tremmel R, Zhou Y, Schwab M, Lauschke VM. Structural variation of the coding and non-coding human pharmacogenome. NPJ Genom Med 2023; 8:24. [PMID: 37684227 PMCID: PMC10491600 DOI: 10.1038/s41525-023-00371-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Genetic variants in drug targets and genes encoding factors involved in drug absorption, distribution, metabolism and excretion (ADME) can have pronounced impacts on drug pharmacokinetics, response, and toxicity. While the landscape of genetic variability at the level of single nucleotide variants (SNVs) has been extensively studied in these pharmacogenetic loci, their structural variation is only poorly understood. Thus, we systematically analyzed the genetic structural variability across 908 pharmacogenes (344 ADME genes and 564 drug targets) based on publicly available whole genome sequencing data from 10,847 unrelated individuals. Overall, we extracted 14,984 distinct structural variants (SVs) ranging in size from 50 bp to 106 Mb. Each individual harbored on average 10.3 and 1.5 SVs with putative functional effects that affected the coding regions of ADME genes and drug targets, respectively. In addition, by cross-referencing pharmacogenomic SVs with experimentally determined binding data of 224 transcription factors across 130 cell types, we identified 1276 non-coding SVs that overlapped with gene regulatory elements. Based on these data, we estimate that non-coding structural variants account for 22% of the genetically encoded pharmacogenomic variability. Combined, these analyses provide the first comprehensive map of structural variability across pharmacogenes, derive estimates for the functional impact of non-coding SVs and incentivize the incorporation of structural genomic data into personalized drug response predictions.
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Affiliation(s)
- Roman Tremmel
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University Tübingen, Tübingen, Germany
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University Tübingen, Tübingen, Germany
- Departments of Clinical Pharmacology and Pharmacy and Biochemistry, University Tübingen, Tübingen, Germany
| | - Volker M Lauschke
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
- University Tübingen, Tübingen, Germany.
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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2
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Vu NP, Nguyen TD, Nguyen BH, Nguyen DT, Nong HV, Nguyen HH. Copy number variations of cytochrome P450 genes in Kinh Vietnamese. ASIAN BIOMED 2023; 17:84-92. [PMID: 37719322 PMCID: PMC10505059 DOI: 10.2478/abm-2023-0048] [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] [Indexed: 09/19/2023]
Abstract
Background The cytochrome P450 (CYP450) family is well known as a major group of drug metabolizing enzymes. The polymorphism of CYP450 genes is the main factor having an impact on the interindividual difference in drug response, including drug efficacy and drug safety. The single nucleotide polymorphism (SNPs) of Vietnamese Kinh has been widely studied, but information about the copy number variations (CNVs) of other CYP450 genes is still unknown. Objective To identify the CNV variability of CYP450 in 154 healthy unrelated Kinh Vietnamese, except eCYP2D6, which was previously reported. Methods Multiplex Ligation-Dependent Probe Amplification (MLPA) was applied for determination of copy number of 10 CYP450 genes. Later, PCR or quantitative PCR (qPCR) was used to confirm the detected CNVs in randomly chosen subjects. Results Of the 154 subjects, along with CYP2D6, 4 other CYP450 genes showed CNVs including duplications (CYP1B1), deletions (CYP2A6 and CYP2C9), and both duplications and deletions (CYP2E1). Among these, CYP2A6 exhibited the greatest frequency of CNVs compared with other CYP450, in which CYP2A6Del accounted for 11%. Meanwhile, allele CYP2E1Del showed the lowest frequency with only 0.3%. Conclusions The present study provides new insight into CYP450 CNVs in the Kinh Vietnamese cohort. Our data have contributed to genetic profiling of CYP450 CNVs in Vietnam, which would be helpful for facilitating implementation of pharmacogenetics in drug dosing adjustment in Vietnam.
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Affiliation(s)
- Nhung Phuong Vu
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
- Genome Analysis Laboratory, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
| | - Ton Dang Nguyen
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
- Genome Analysis Laboratory, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
| | - Binh Huy Nguyen
- Department of Physiology, Hanoi Medical University, Dong Da, Hanoi100000, Vietnam
| | - Duong Thuy Nguyen
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
- Genome Analysis Laboratory, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
| | - Hai Van Nong
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
- Genome Analysis Laboratory, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
| | - Ha Hai Nguyen
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
- Genome Analysis Laboratory, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
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Koubek EJ, Ralya AT, Larson TR, McGovern RM, Buhrow SA, Covey JM, Adjei AA, Takebe N, Ames MM, Goetz MP, Reid JM. Population Pharmacokinetics of Z-Endoxifen in Patients With Advanced Solid Tumors. J Clin Pharmacol 2022; 62:1121-1131. [PMID: 35358345 PMCID: PMC9339467 DOI: 10.1002/jcph.2053] [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: 01/18/2022] [Accepted: 03/24/2022] [Indexed: 11/11/2022]
Abstract
The purpose of this study was to develop and validate a population pharmacokinetic model for Z-endoxifen in patients with advanced solid tumors and to identify clinical variables that influence pharmacokinetic parameters. Z-endoxifen-HCl was administered orally once a day on a 28-day cycle (±3 days) over 11 dose levels ranging from 20 to 360 mg. A total of 1256 Z-endoxifen plasma concentration samples from 80 patients were analyzed using nonlinear mixed-effects modeling to develop a population pharmacokinetic model for Z-endoxifen. A 2-compartment model with oral depot and linear elimination adequately described the data. The estimated apparent total clearance, apparent central volume of distribution, and apparent peripheral volume of distribution were 4.89 L/h, 323 L, and 39.7 L, respectively, with weight-effect exponents of 0.75, 1, and 1, respectively. This model was used to explore the effects of clinical and demographic variables on Z-endoxifen pharmacokinetics. Weight, race on clearance, and aspartate aminotransferase on the absorption rate constant were identified as significant covariates in the final model. This novel population pharmacokinetic model provides insight regarding factors that may affect the pharmacokinetics of Z-endoxifen and may assist in the design of future clinical trials.
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Affiliation(s)
- Emily J. Koubek
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Thomas R. Larson
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
- Molecular Pharmacology and Experimental Therapeutics Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, USA
| | | | - Sarah A. Buhrow
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Alex A. Adjei
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Pharmacology, Mayo Clinic, Rochester, Minnesota, USA
| | - Naoko Takebe
- National Cancer Institute, Bethesda, Maryland, USA
| | - Matthew M. Ames
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Pharmacology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew P. Goetz
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Pharmacology, Mayo Clinic, Rochester, Minnesota, USA
| | - Joel M. Reid
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Pharmacology, Mayo Clinic, Rochester, Minnesota, USA
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Simple and Robust Detection of CYP2D6 Gene Deletions and Duplications Using CYP2D8P as Reference. Pharmaceuticals (Basel) 2022; 15:ph15020166. [PMID: 35215279 PMCID: PMC8880347 DOI: 10.3390/ph15020166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/23/2022] [Accepted: 01/27/2022] [Indexed: 12/04/2022] Open
Abstract
Genotyping of the CYP2D6 gene is the most commonly applied pharmacogenetic test globally. Significant economic interests have led to the development of a plurality of assays, available for almost any genotyping platform or DNA detection chemistry. Of all the genetic variants, copy number variations are particular difficult to detect by polymerase chain reaction. Here, we present two simple novel approaches for the identification of samples carrying either deletions or duplications of the CYP2D6 gene; by relative quantification using a singleplex 5′nuclease real-time PCR assay, and by high-resolution melting of PCR products. These methods make use of universal primers, targeting both the CYP2D6 and the reference gene CYP2D8P, which is necessary for the analysis. The assays were validated against a reference method using a large set of samples. The singleplex nature of the 5′nuclease real-time PCR ensures that the primers anneal with equal affinity to both the sequence of the CYP2D6 and the reference gene. This facilitates robust identification of gene deletions and duplications based on the cycle threshold value. In contrast, the high-resolution melting assay is an end-point PCR, where the identification relies on variations between the amount of product generated from each of the two genes.
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Ahsan T, Shoily SS, Fatema K, Sajib AA. Impacts of 119 missense variants at functionally important sites of drug-metabolizing human cytosolic sulfotransferase SULT1A1: An in silico study. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2021.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Han N, Oh JM, Kim IW. Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans. J Pers Med 2021; 11:33. [PMID: 33430289 PMCID: PMC7825650 DOI: 10.3390/jpm11010033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/16/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022] Open
Abstract
For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (N = 72,299) and CNV data (N = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. CYP2D6 rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. DMD ranked the highest in frequency for gene gain (64.52%), while TPMT ranked the highest in frequency for gene loss (51.80%). Copy number gain of CYP4F2 was observed in 22 subjects; 13 of those subjects were carriers with CYP4F2*3 gain. In the case of TPMT, approximately one-half of the participants (N = 308) had loss of the TPMT*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.
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Affiliation(s)
| | | | - In-Wha Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea; (N.H.); (J.M.O.)
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Ebrahimizadeh W, Guérard KP, Rouzbeh S, Bramhecha YM, Scarlata E, Brimo F, Patel PG, Jamaspishvili T, Aprikian AG, Berman D, Bartlett JMS, Chevalier S, Lapointe J. Design and Development of a Fully Synthetic Multiplex Ligation-Dependent Probe Amplification-Based Probe Mix for Detection of Copy Number Alterations in Prostate Cancer Formalin-Fixed, Paraffin-Embedded Tissue Samples. J Mol Diagn 2020; 22:1246-1263. [PMID: 32763409 DOI: 10.1016/j.jmoldx.2020.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/24/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
DNA copy number alterations (CNAs) are promising biomarkers to predict prostate cancer (PCa) outcome. However, fluorescence in situ hybridization (FISH) cannot assess complex CNA signatures because of low multiplexing capabilities. Multiplex ligation-dependent probe amplification (MLPA) can detect multiple CNAs in a single PCR assay, but PCa-specific probe mixes available commercially are lacking. Synthetic MLPA probes were designed to target 10 CNAs relevant to PCa: 5q15-21.1 (CHD1), 6q15 (MAP3K7), 8p21.2 (NKX3-1), 8q24.21 (MYC), 10q23.31 (PTEN), 12p13.1 (CDKN1B), 13q14.2 (RB1), 16p13.3 (PDPK1), 16q23.1 (GABARAPL2), and 17p13.1 (TP53), with 9 control probes. In cell lines, CNAs were detected when the cancer genome was as low as 30%. Compared with FISH in radical prostatectomy formalin-fixed, paraffin-embedded samples (n = 18: 15 cancers and 3 matched benign), the MLPA assay showed median sensitivity and specificity of 80% and 93%, respectively, across all CNAs assessed. In the validation set (n = 40: 20 tumors sampled in two areas), the respective sensitivity and specificity of MLPA compared advantageously with FISH and TaqMan droplet digital PCR (ddPCR) when assessing PTEN deletion (FISH: 85% and 100%; ddPCR: 100% and 83%) and PDPK1 gain (FISH: 100% and 92%; ddPCR: 93% and 100%). This new PCa probe mix accurately identifies CNAs by MLPA across multiple genes using low quality and quantities (50 ng) of DNA extracted from clinical formalin-fixed, paraffin-embedded samples.
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Affiliation(s)
- Walead Ebrahimizadeh
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Karl-Philippe Guérard
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Shaghayegh Rouzbeh
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Yogesh M Bramhecha
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Eleonora Scarlata
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Fadi Brimo
- Department of Pathology, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Palak G Patel
- Department of Pathology, Queen's University, Kingston, Ontario, Canada
| | | | - Armen G Aprikian
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - David Berman
- Department of Pathology, Queen's University, Kingston, Ontario, Canada
| | - John M S Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Simone Chevalier
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Jacques Lapointe
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
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Botton MR, Lu X, Zhao G, Repnikova E, Seki Y, Gaedigk A, Schadt EE, Edelmann L, Scott SA. Structural variation at the CYP2C locus: Characterization of deletion and duplication alleles. Hum Mutat 2020; 40:e37-e51. [PMID: 31260137 DOI: 10.1002/humu.23855] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/11/2019] [Accepted: 06/25/2019] [Indexed: 12/27/2022]
Abstract
The human CYP2C locus harbors the polymorphic CYP2C18, CYP2C19, CYP2C9, and CYP2C8 genes, and of these, CYP2C19 and CYP2C9 are directly involved in the metabolism of ~15% of all medications. All variant CYP2C19 and CYP2C9 star (*) allele haplotypes currently cataloged by the Pharmacogene Variation (PharmVar) Consortium are defined by sequence variants. To determine if structural variation also occurs at the CYP2C locus, the 10q23.33 region was interrogated across deidentified clinical chromosomal microarray (CMA) data from 20,642 patients tested at two academic medical centers. Fourteen copy number variants that affected the coding region of CYP2C genes were detected in the clinical CMA cohorts, which ranged in size from 39.2 to 1,043.3 kb. Selected deletions and duplications were confirmed by MLPA or ddPCR. Analysis of the clinical CMA and an additional 78,839 cases from the Database of Genomic Variants (DGV) and ClinGen (total n = 99,481) indicated that the carrier frequency of a CYP2C structural variant is ~1 in 1,000, with ~1 in 2,000 being a CYP2C19 full gene or partial-gene deletion carrier, designated by PharmVar as CYP2C19*36 and *37, respectively. Although these structural variants are rare in the general population, their detection will likely improve metabolizer phenotype prediction when interrogated for research and/or clinical testing.
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Affiliation(s)
- Mariana R Botton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Xingwu Lu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Geping Zhao
- Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Elena Repnikova
- Clinical Genetics and Genomics Laboratories, Children's Mercy Hospital Kansas City, Kansas City, Missouri.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | | | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
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Abstract
Sulfur is present in the amino acids cysteine and methionine and in a large range of essential coenzymes and cofactors and is therefore essential for all organisms. It is also a constituent of sulfate esters in proteins, carbohydrates, and numerous cellular metabolites. The sulfation and desulfation reactions modifying a variety of different substrates are commonly known as sulfation pathways. Although relatively little is known about the function of most sulfated metabolites, the synthesis of activated sulfate used in sulfation pathways is essential in both animal and plant kingdoms. In humans, mutations in the genes encoding the sulfation pathway enzymes underlie a number of developmental aberrations, and in flies and worms, their loss-of-function is fatal. In plants, a lower capacity for synthesizing activated sulfate for sulfation reactions results in dwarfism, and a complete loss of activated sulfate synthesis is also lethal. Here, we review the similarities and differences in sulfation pathways and associated processes in animals and plants, and we point out how they diverge from bacteria and yeast. We highlight the open questions concerning localization, regulation, and importance of sulfation pathways in both kingdoms and the ways in which findings from these "red" and "green" experimental systems may help reciprocally address questions specific to each of the systems.
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Affiliation(s)
- Süleyman Günal
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne 50674, Germany
| | - Rebecca Hardman
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne 50674, Germany.
| | - Jonathan Wolf Mueller
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham B15 2TH, United Kingdom.
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