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Thamilselvan M, Mather C, Wang Y, Foo JC, Aitchison KJ. Haplotype phasing of CYP2D6: an allelic ratio method using Agena MassARRAY data. Transl Psychiatry 2024; 14:91. [PMID: 38346976 PMCID: PMC10861455 DOI: 10.1038/s41398-024-02809-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/15/2024] Open
Abstract
Pharmacogenomics aims to use the genetic information of an individual to personalize drug prescribing. There is evidence that pharmacogenomic testing before prescription may prevent adverse drug reactions, increase efficacy, and reduce cost of treatment. CYP2D6 is a key pharmacogene of relevance to multiple therapeutic areas. Indeed, there are prescribing guidelines available for medications based on CYP2D6 enzyme activity as deduced from CYP2D6 genetic data. The Agena MassARRAY system is a cost-effective method of detecting genetic variation that has been clinically applied to other genes. However, its clinical application to CYP2D6 has to date been limited by weaknesses such as the inability to determine which haplotype was present in more than one copy for individuals with more than two copies of the CYP2D6 gene. We report application of a new protocol for CYP2D6 haplotype phasing of data generated from the Agena MassARRAY system. For samples with more than two copies of the CYP2D6 gene for which the prior consensus data specified which one was present in more than one copy, our protocol was able to conduct CYP2D6 haplotype phasing resulting in 100% concordance with the prior data. In addition, for three reference samples known to have more than two copies of CYP2D6 but for which the exact number of CYP2D6 genes was unknown, our protocol was able to resolve the number for two out of the three of these, and estimate the likely number for the third. Finally, we demonstrate that our method is applicable to CYP2D6 hybrid tandem configurations.
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Affiliation(s)
- Megana Thamilselvan
- University of Alberta, College of Natural and Applied Sciences, Department of Biological Sciences, Edmonton, Canada
| | - Cheryl Mather
- University of Alberta, College of Health Sciences, Department of Laboratory Medicine and Pathology, Edmonton, Canada
- Alberta Precision Laboratories, Edmonton, Canada
| | - Yabing Wang
- University of Alberta, College of Health Sciences, Department of Psychiatry, Edmonton, Canada
| | - Jerome C Foo
- University of Alberta, College of Health Sciences, Department of Psychiatry, Edmonton, Canada
| | - Katherine J Aitchison
- University of Alberta, College of Health Sciences, Department of Psychiatry, Edmonton, Canada.
- University of Alberta, Neuroscience and Mental Health Institute, Edmonton, Canada.
- University of Alberta, College of Health Sciences, Department of Medical Genetics, Edmonton, Canada.
- Northern Ontario School of Medicine, Thunder Bay, Canada.
- University of Alberta, Women and Children's Health Research Institute, Edmonton, Canada.
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Kim S, Kim JM, Lee HJ, Lim JS, Seong IO, Kim KH. Alteration of CYP4A11 expression in renal cell carcinoma: diagnostic and prognostic implications. J Cancer 2020; 11:1478-1485. [PMID: 32047554 PMCID: PMC6995385 DOI: 10.7150/jca.36438] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 12/01/2019] [Indexed: 01/08/2023] Open
Abstract
Background: Cytochrome P-450 4A11 (CYP4A11) and peroxisome proliferator-activated receptor-α (PPARα) are expressed at high levels in renal proximal tubules, and upregulation of CYP4A11 protein levels is known to be influenced by PPAR agonists. The goal of this study was to evaluate the clinicopathological role of CYP4A11 expression in renal cell carcinoma (RCC). Methods: We performed immunohistochemical analysis of CYP4A11, CYP4A22 and PPARα and correlated the results with the clinicopathological features of RCC (n=139). Reverse transcription digital droplet polymerase chain reaction (RT-ddPCR) against CYP4A11 and CYP4A22 was also performed. Results: CYP4A11 mRNA expression levels were higher in non-neoplastic kidney tissues than in matched tumor tissues in 12 matched pairs of freshly frozen primary clear-cell RCC (ccRCC) and nontumor tissue (p=0.002). Immunohistochemical staining showed that CYP4A11 expression was significantly lower in ccRCC than in non-ccRCCs, including papillary, chromophobe, and unclassified RCCs (p<0.001). CYP4A11 expression was associated with PPARα expression, males and high nuclear histologic grades (p=0.001, p=0.018 and p<0.001). Univariate and multivariate analyses revealed that CYP4A11 expression was correlated with short overall survival (p=0.007 and p=0.010). Conclusion: These findings suggest that CYP4A11 expression is a potential poor prognostic factor of RCC. The considerable decrease in CYP4A11 expression is a predictive diagnostic factor of ccRCC, and CYP4A11 metabolism in ccRCC might be different from that in non-ccRCCs.
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Affiliation(s)
- Sup Kim
- Department of Radiation Oncology, Chungnam National University Hospital, Daejeon, South Korea
| | - Jin Man Kim
- Department of Pathology/Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Hyo Jin Lee
- Division of Hematology/Oncology, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Jae Sung Lim
- Department of Urology, Chungnam National University School of Medicine, Daejeon, South Korea
| | - In-Ock Seong
- Department of Pathology/Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Kyung-Hee Kim
- Department of Pathology/Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
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Gaedigk A, Turner A, Everts RE, Scott SA, Aggarwal P, Broeckel U, McMillin GA, Melis R, Boone EC, Pratt VM, Kalman LV. Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles: A GeT-RM Collaborative Project. J Mol Diagn 2019; 21:1034-1052. [PMID: 31401124 DOI: 10.1016/j.jmoldx.2019.06.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/10/2019] [Accepted: 06/13/2019] [Indexed: 11/25/2022] Open
Abstract
Pharmacogenetic testing increasingly is available from clinical and research laboratories. However, only a limited number of quality control and other reference materials currently are available for the complex rearrangements and rare variants that occur in the CYP2D6 gene. To address this need, the Division of Laboratory Systems, CDC-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Cell Repositories (Camden, NJ), has characterized 179 DNA samples derived from Coriell cell lines. Testing included the recharacterization of 137 genomic DNAs that were genotyped in previous Genetic Testing Reference Material Coordination Program studies and 42 additional samples that had not been characterized previously. DNA samples were distributed to volunteer testing laboratories for genotyping using a variety of commercially available and laboratory-developed tests. These publicly available samples will support the quality-assurance and quality-control programs of clinical laboratories performing CYP2D6 testing.
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Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Amy Turner
- Medical College of Wisconsin, Milwaukee, Wisconsin; RPRD (Right Patient Right Drug) Diagnostics, LLC, Wauwatosa, Wisconsin
| | | | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Sema4, Stamford, Connecticut
| | - Praful Aggarwal
- Medical College of Wisconsin, Milwaukee, Wisconsin; RPRD (Right Patient Right Drug) Diagnostics, LLC, Wauwatosa, Wisconsin
| | - Ulrich Broeckel
- Medical College of Wisconsin, Milwaukee, Wisconsin; RPRD (Right Patient Right Drug) Diagnostics, LLC, Wauwatosa, Wisconsin
| | | | | | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Lisa V Kalman
- Informatics and Data Science Branch, Division of Laboratory Systems, Office of Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, Georgia.
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Eun HS, Cho SY, Lee BS, Kim S, Song IS, Chun K, Oh CH, Yeo MK, Kim SH, Kim KH. Cytochrome P450 4A11 expression in tumor cells: A favorable prognostic factor for hepatocellular carcinoma patients. J Gastroenterol Hepatol 2019; 34:224-233. [PMID: 30069903 DOI: 10.1111/jgh.14406] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/10/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM Elevated cytochrome p450 (CYP) 4A gene expression has been linked to the aggravation of various cancers and affects various regulated metabolites. In hepatocellular carcinoma (HCC), the clinicopathological value of CYP4A has not yet been explored, although CYP4A is expressed at high levels in the liver. The goal of this study was to evaluate the clinicopathological value of CYP4A11 expression in HCC. METHODS We performed immunohistochemical analysis of CYP4A11 and correlated the results with clinicopathological features of HCC (n = 155). Western blotting and reverse transcription-polymerase chain reaction against CYP4A11 and CYP4A22 were also performed for 15 and 20 pairs of fresh-frozen primary HCC and non-neoplastic liver tissue, respectively. Moreover, we analyzed the underlying mechanism by comparing the high and low CYP4A11 mRNA expression groups using gene set enrichment analysis. RESULTS CYP4A11 expression level was higher in non-neoplastic hepatocytes than those in HCC cells (P < 0.001), and CYP4A11 expression positively correlated with favorable prognostic factors, including tumor size, histological grade, and pathological tumor stage (P = 0.007, P = 0.005, and P = 0.007). Multivariate analysis revealed that CYP4A11 expression was an independent prognostic factor of overall and disease-free survival (P = 0.002 and P = 0.033). Based on gene set enrichment analysis, high CYP4A11 mRNA expression negatively correlated with the expression of cell cycle-related genes. CONCLUSION These findings support the notion that CYP4A11 expression is a favorable prognostic factor of HCC and suggest potential predictive diagnostic and prognostic roles of CYP4A11 expression in HCC.
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Affiliation(s)
- Hyuk Soo Eun
- Department of Internal Medicine, Chungnam National University Hospital, Daejeon, Korea.,Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Sang Yeon Cho
- College of Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Byung Seok Lee
- Department of Internal Medicine, Chungnam National University Hospital, Daejeon, Korea.,Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Sup Kim
- Department of Microbiology, Infection Control Convergence Research Center, Medical Science, Radiation Oncology, Chungnam National University School of Medicine, Daejeon, Korea
| | - In-Sang Song
- Department of Surgery, Chungnam National University Hospital, Daejeon, Korea.,Department of Surgery, Chungnam National University School of Medicine, Daejeon, Korea
| | - Kwangsik Chun
- Department of Surgery, Chungnam National University Hospital, Daejeon, Korea.,Department of Surgery, Chungnam National University School of Medicine, Daejeon, Korea
| | - Cheong-Hae Oh
- Department of Internal Medicine, Chungnam National University Hospital, Daejeon, Korea.,Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, Korea
| | - Seok Hyun Kim
- Department of Internal Medicine, Chungnam National University Hospital, Daejeon, Korea.,Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Kyung-Hee Kim
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, Korea
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