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Rahmayanti SU, Amalia R, Rusdiana T. Systematic review: genetic polymorphisms in the pharmacokinetics of high-dose methotrexate in pediatric acute lymphoblastic leukemia patients. Cancer Chemother Pharmacol 2024:10.1007/s00280-024-04694-0. [PMID: 39002021 DOI: 10.1007/s00280-024-04694-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 06/25/2024] [Indexed: 07/15/2024]
Abstract
Variations in pharmacokinetic responses to high-dose methotrexate are essential for the prognosis and management of toxicity in the treatment of pediatric acute lymphoblastic leukemia (ALL) patients. This systematic review aimed to identify and evaluate genetic polymorphisms that are significantly associated with the pharmacokinetic parameters of methotrexate during the consolidation phase of pediatric ALL treatment. Using the Preferred Reporting Items for Systematic Reviews (PRISMA) guidelines, we systematically reviewed the literature from 2013 to 2023. The databases used were PubMed and Scopus. The outcomes of interest are the study design, patient characteristics, sample size, chemotherapy protocol utilized, pharmacokinetic parameters identified, and genetic polymorphisms implicated. We included 31 articles in the qualitative synthesis and found that the SLCO1B1, ABCB1, ABCC2, and MTHFR genes appear to play significant roles in MTX metabolism and clearance. Among these, variations in SLCO1B1 have the most significant and consistent impact on methotrexate clearance. These implicated variants may contribute to the precision and tailoring of HD-MTX treatment in pediatric ALL patients.
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Affiliation(s)
- Siti Utami Rahmayanti
- Master Program in Pharmacy, Faculty of Pharmacy, Padjadjaran University, Sumedang, West Java, 45363, Indonesia
| | - Riezki Amalia
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Padjadjaran University, Sumedang, 45363, Indonesia
| | - Taofik Rusdiana
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Padjadjaran University, Sumedang, 45363, Indonesia.
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Hong DZ, Ong TCC, Timbadia DP, Tan HTA, Kwa ED, Chong WQ, Goh BC, Loh WS, Loh KS, Tan EC, Tay JK. Systematic Review and Meta-Analysis of the Influence of Genetic Variation on Ototoxicity in Platinum-Based Chemotherapy. Otolaryngol Head Neck Surg 2023; 168:1324-1337. [PMID: 36802061 DOI: 10.1002/ohn.222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 11/04/2022] [Accepted: 11/19/2022] [Indexed: 02/19/2023]
Abstract
OBJECTIVE The objective of this meta-analysis is to evaluate the impact of genetic polymorphisms on platinum-based chemotherapy (PBC)-induced ototoxicity. DATA SOURCES Systematic searches of PubMed, Embase, Cochrane, and Web of Science were conducted from the inception of the databases to May 31, 2022. Abstracts and presentations from conferences were also reviewed. REVIEW METHODS Four investigators independently extracted data in adherence to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Differences in the prevalence of PBC-induced ototoxicity between reference and variant (i) genotypes and (ii) alleles were analyzed. The overall effect size was presented using the random-effects model as an odds ratio (OR) with a 95% confidence interval (CI). RESULTS From 32 included articles, 59 single nucleotide polymorphisms on 28 genes were identified, with 4406 total unique participants. For allele frequency analysis, the A allele in ACYP2 rs1872328 was positively associated with ototoxicity (OR: 2.61; 95% CI: 1.06-6.43; n = 2518). Upon limiting to cisplatin use only, the T allele of COMT rs4646316 and COMT rs9332377 revealed significant results. For genotype frequency analysis, the CT/TT genotype in ERCC2 rs1799793 demonstrated an otoprotective effect (OR: 0.50; 95% CI: 0.27-0.94; n = 176). Excluding studies using carboplatin or concomitant radiotherapy revealed significant effects with COMT rs4646316, GSTP1 rs1965, and XPC rs2228001. Major sources of variations between studies include differences in patient demographics, ototoxicity grading systems, and treatment protocols. CONCLUSION Our meta-analysis presents polymorphisms that exert ototoxic or otoprotective effects in patients undergoing PBC. Importantly, several of these alleles are observed at high frequencies globally, highlighting the potential for polygenic screening and cumulative risk evaluation for personalized care.
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Affiliation(s)
- Daniel Z Hong
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore, Singapore
| | - Thaned C C Ong
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore, Singapore
| | - Dhayan P Timbadia
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore, Singapore
| | - Hui T A Tan
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore, Singapore
| | - Eunice D Kwa
- Department of Otolaryngology-Head and Neck Surgery, National University Hospital, Singapore, Singapore
| | - Wan Q Chong
- Department of Haematology-Oncology, National University Hospital, Singapore, Singapore
| | - Boon C Goh
- Department of Haematology-Oncology, National University Hospital, Singapore, Singapore
| | - Woei S Loh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore, Singapore
- Department of Otolaryngology-Head and Neck Surgery, National University Hospital, Singapore, Singapore
| | - Kwok S Loh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore, Singapore
- Department of Otolaryngology-Head and Neck Surgery, National University Hospital, Singapore, Singapore
| | - Ene C Tan
- KK Research Centre, KK Women's and Children's Hospital, Singapore, Singapore
| | - Joshua K Tay
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore, Singapore
- Department of Otolaryngology-Head and Neck Surgery, National University Hospital, Singapore, Singapore
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3
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Association between ABCC2 polymorphism and hematological toxicity in patients with esophageal cancer receiving platinum plus 5-fluorouracil therapy. Esophagus 2022; 19:146-152. [PMID: 34347217 DOI: 10.1007/s10388-021-00865-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/28/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND Platinum agents are taken up into cells by copper transporter (CTR) 1 (gene code: SLC31A1) and are excreted from cells by copper-transporting P-type adenosine triphosphatase (ATP7B) and multidrug resistance-associated protein (MRP) 2 (gene code: ABCC2). In addition, glutathione S transferase (GST) P1 is involved in the metabolism of platinum agents. The present study aimed to determine whether the rate of grade 3-4 hematological toxicity associated with platinum plus 5-fluorouracil (5-FU) therapy in 239 patients with esophageal cancer was affected by the SLC31A1 rs10981694A>C and rs12686377G>T, ATP7B rs9535828A>G, GSTP1 rs1695A>G, and ABCC2 -24C>T polymorphisms. METHODS Chemotherapy consisted of protracted infusion of 5-FU (800 mg/m2/day) on days 1-5 and cisplatin or nedaplatin (80 mg/m2/day) on day 1. RESULTS A total of 82 of 239 patients developed grade 3-4 hematological toxicity after chemotherapy. Univariate analysis showed that ABCC2 -24C/T + T/T genotypes (P = 0.038), radiation therapy (P = 0.013), baseline white blood cell count < 6000/μL (P = 0.003), and baseline neutrophil count < 3900/μL (P = 0.021) were statistically significant predictors of grade 3-4 hematological toxicity. Multivariate analysis revealed that ABCC2 -24C/T + T/T genotypes (P = 0.036), radiation therapy (P = 0.005), and baseline white blood cell count < 6000/μL (P < 0.001) were significant risk factors. CONCLUSIONS We determined that ABCC2 -24C>T is significantly associated with grade 3-4 hematological toxicity after platinum plus 5-FU therapy. These findings might contribute to improved treatment strategies for patients with esophageal cancer.
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Al-Mahayri ZN, AlAhmad MM, Ali BR. Current opinion on the pharmacogenomics of paclitaxel-induced toxicity. Expert Opin Drug Metab Toxicol 2021; 17:785-801. [PMID: 34128748 DOI: 10.1080/17425255.2021.1943358] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Paclitaxel is a microtubule stabilizer that is currently one of the most utilized chemotherapeutic agents. Its efficacy in breast, uterine, lung and other neoplasms made its safety profile enhancement a subject of great interest. Neurotoxicity is the most common paclitaxel-associated toxicities. In addition, hypersensitivity reactions, hematological, gastrointestinal, and cardiac toxicities are all encountered.Areas covered: The current review explores paclitaxel-induced toxicities mechanisms and risk factors. Studies investigating these toxicities pharmacogenomic biomarkers are reviewed and summarized. There is a limited margin of consistency between the retrieved associations. Variants in genes related to neuro-sensitivity are the most promising candidates for future studies.Expert opinion: Genome-wide association studies highlighted multiple-candidate biomarkers relevant to neuro-sensitivity. Most of the identified paclitaxel-neurotoxicity candidate genes are derived from congenital neuropathy and diabetic-induced neurotoxicity pathways. Future studies should explore these sets of genes while considering the multifactorial nature of paclitaxel-induced neurotoxicity. In the absence of certain paclitaxel-toxicity biomarkers, future research should avoid earlier studies' caveats. Genes in paclitaxel's pharmacokinetic pathways could not provide consistent results in any of its associated toxicities. There is a need to dig deeper into toxicity-development mechanisms and personal vulnerability factors, rather than targeting only the genes suspected to affect drug exposure.
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Affiliation(s)
- Zeina N Al-Mahayri
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Mohammad M AlAhmad
- Department of Clinical Pharmacy, College of Pharmacy, Al-Ain University, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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An Example of Personalized Treatment in HR+ HER2+ Long Survivor Breast Cancer Patient (Case Report). Curr Oncol 2021; 28:1980-1987. [PMID: 34070464 PMCID: PMC8161821 DOI: 10.3390/curroncol28030184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/12/2021] [Accepted: 05/16/2021] [Indexed: 12/13/2022] Open
Abstract
Background. Personalized therapy is becoming increasingly popular in oncological scenarios, not only based on molecular pharmacological targets, but also preventing any drug–drug–gene interaction (DDGI), which could lead to severe toxicities. Single nucleotide polymorphisms (SNPs), the individual germline sequence variations in genes involved in drug metabolism, are correlated to interindividual response to drugs and explain both efficacy and toxicity profiles reported by patients. Case presentation. We present the case of a woman suffering from triple-positive breast cancer; she had early-stage disease at the onset and after four years developed metastatic disease. During her history, she presented different toxicities due to antineoplastic treatments. Particularly, hypertransaminasemia was found during every line of treatment. Nevertheless, we were able to guarantee the patient an excellent therapeutic adhesion thanks to the supportive treatments and the reduction of drug dosage. Moreover, we conducted a simultaneous analysis of the patient’s biochemical and genomic data thanks to Drug-PIN software, and we found several significant SNPs of the main enzymes and transporters involved in drug metabolism. Conclusion. Our case report demonstrated the relevance of DDGI in clinical practice management of a patient treated for advanced breast cancer, suggesting the role of Drug-PIN software as an easy-to-use tool to prevent adverse events during cancer treatment and to help physicians in therapeutic algorithms. However, further studies are needed to confirm these results.
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Bhat A, Bhat GR, Verma S, Sharma B, Bakshi D, Abrol D, Singh S, Qadri RA, Shah R, Kumar R. Evaluation of 17 genetic variants in association with leukemia in the north Indian population using MassARRAY Sequenom. J Biochem Mol Toxicol 2021; 35:e22792. [PMID: 33928715 DOI: 10.1002/jbt.22792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/29/2021] [Accepted: 04/08/2021] [Indexed: 12/24/2022]
Abstract
Leukemia is a heterogeneous disorder, characterized by elevated proliferation of white blood cells. In this study, we explored the association of 17 genetic variants with leukemia patients in the Jammu and Kashmir region of north India. The variants were genotyped by using a high-throughput Agena MassARRAY platform in 758 individuals (166 cases and 592 controls). Of the 17 single-nucleotide polymorphisms (SNPs) studied, five SNPs were showing significant association with the high risk of leukemia in the north Indian population, which includes rs10069690 of telomere reverse transcriptase (TERT) with OR = 0.34 (95% CI, 0.20-0.58; p = .0008), rs2972392 (PSCA) with OR 1.86 (95% CI, 1.04-3.81; p = .035), rs4986764 (BRIP1) with OR 1.34 (95% CI, 1.00-1.80; p = .04), rs6990097 (TNKS) with OR 1.81 (95% CI, 1.2-2.6; p = .001) and rs12190287 (TCF21) with OR 2.87 (95% CI, 1.72-4.7; p = .0001) by allelic association using Plink and analyzed by SPSS. This is the first study to explore these variants with leukemia in the studied population.
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Affiliation(s)
- Amrita Bhat
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Gh Rasool Bhat
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Sonali Verma
- ICMR-CAR, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Bhanu Sharma
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Divya Bakshi
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Deepak Abrol
- Department of Radiotherapy, Government Medical College Kathua, Jammu and Kashmir, India
| | - Supinder Singh
- Department of Medicine, ASCOMS, Sidhra, Jammu and Kashmir, India
| | | | - Ruchi Shah
- ICMR-CAR, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Rakesh Kumar
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
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7
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Prevalence of pharmacogenomic variants in 100 pharmacogenes among Southeast Asian populations under the collaboration of the Southeast Asian Pharmacogenomics Research Network (SEAPharm). Hum Genome Var 2021; 8:7. [PMID: 33542200 PMCID: PMC7862625 DOI: 10.1038/s41439-021-00135-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 02/08/2023] Open
Abstract
Pharmacogenomics can enhance the outcome of treatment by adopting pharmacogenomic testing to maximize drug efficacy and lower the risk of serious adverse events. Next-generation sequencing (NGS) is a cost-effective technology for genotyping several pharmacogenomic loci at once, thereby increasing publicly available data. A panel of 100 pharmacogenes among Southeast Asian (SEA) populations was resequenced using the NGS platform under the collaboration of the Southeast Asian Pharmacogenomics Research Network (SEAPharm). Here, we present the frequencies of pharmacogenomic variants and the comparison of these pharmacogenomic variants among different SEA populations and other populations used as controls. We investigated the different types of pharmacogenomic variants, especially those that may have a functional impact. Our results provide substantial genetic variations at 100 pharmacogenomic loci among SEA populations that may contribute to interpopulation variability in drug response phenotypes. Correspondingly, this study provides basic information for further pharmacogenomic investigations in SEA populations.
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8
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Ferracini AC, Lopes-Aguiar L, Lourenço GJ, Yoshida A, Lima CSP, Sarian LO, Derchain S, Kroetz DL, Mazzola PG. GSTP1 and ABCB1 Polymorphisms Predicting Toxicities and Clinical Management on Carboplatin and Paclitaxel-Based Chemotherapy in Ovarian Cancer. Clin Transl Sci 2020; 14:720-728. [PMID: 33326171 PMCID: PMC7993324 DOI: 10.1111/cts.12937] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022] Open
Abstract
Variation in drug disposition genes might contribute to susceptibility to toxicities and interindividual differences in clinical management on chemotherapy for epithelial ovarian cancer (EOC). This study was designed to explore the association of GST and ABCB1 genetic variation with hematologic and neurologic toxicity, changes in chemotherapy, and disease prognosis in Brazilian women with EOC. A total of 112 women with a confirmed histological diagnosis of EOC treated with carboplatin/paclitaxel were enrolled (2014–2019). The samples were analyzed by multiplex polymerase chain reaction (PCR) for the deletion of GSTM1 and GSTT1 genes. GSTP1 (c.313A>G/rs1695) and ABCB1 (c.1236C>T/rs1128503; c.3435C>T/rs1045642; c.2677G>T>A/rs2032582) single nucleotide polymorphisms (SNPs) were detected by real‐time PCR. Subjects with the GSTP1 c.313A>G had reduced risk of anemia (odds ratio (OR): 0.17, 95% confidence interval (CI): 0.04–0.69, P = 0.01, dominant model) and for thrombocytopenia (OR: 0.27, 95% CI: 0.12–0.64, P < 0.01; OR 0.18, 95% CI 0.03–0.85, P = 0.03, either dominant or recessive model), respectively. The GSTP1 c.313A>G AG genotype was associated with a lower risk of dose delay (OR: 0.35, 95% CI: 0.13–0.90, P = 0.03). The ABCB1 c.1236C>T was associated with increased risk of thrombocytopenia (OR: 0.15, 95% CI: 0.03–0.82, P = 0.03), whereas ABCB1 c.3435C>T had increased risk of grade 2 and 3 neurotoxicity (OR: 3.61, 95% CI: 1.08–121.01, P = 0.03) in recessive model (CC + CT vs. TT). This study suggests that GSTP1 c.313A>G, ABCB1 c.1236C>T, and c.3435C>T SNP detection is a potential predictor of hematological toxicity and neurotoxicity and could help predict the clinical management of women with EOC.
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Affiliation(s)
- Amanda Canato Ferracini
- Postgraduate Program in Medical Sciences, Faculty of Medical Sciences, University of Campinas, Campinas, Brazil.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Leisa Lopes-Aguiar
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, State University of Campinas, Campinas, Brazil
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, State University of Campinas, Campinas, Brazil
| | - Adriana Yoshida
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, State University of Campinas, Campinas, Brazil
| | - Carmen Silva Passos Lima
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, State University of Campinas, Campinas, Brazil
| | - Luis Otávio Sarian
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, State University of Campinas, Campinas, Brazil
| | - Sophie Derchain
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, State University of Campinas, Campinas, Brazil
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
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Al-Mahayri ZN, Patrinos GP, Wattanapokayakit S, Iemwimangsa N, Fukunaga K, Mushiroda T, Chantratita W, Ali BR. Variation in 100 relevant pharmacogenes among emiratis with insights from understudied populations. Sci Rep 2020; 10:21310. [PMID: 33277594 PMCID: PMC7718919 DOI: 10.1038/s41598-020-78231-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023] Open
Abstract
Genetic variations have an established impact on the pharmacological response. Investigating this variation resulted in a compilation of variants in "pharmacogenes". The emergence of next-generation sequencing facilitated large-scale pharmacogenomic studies and exhibited the extensive variability of pharmacogenes. Some rare and population-specific variants proved to be actionable, suggesting the significance of population pharmacogenomic research. A profound gap exists in the knowledge of pharmacogenomic variants enriched in some populations, including the United Arab Emirates (UAE). The current study aims to explore the landscape of variations in relevant pharmacogenes among healthy Emiratis. Through the resequencing of 100 pharmacogenes for 100 healthy Emiratis, we identified 1243 variants, of which 63% are rare (minor allele frequency ≤ 0.01), and 30% were unique. Filtering the variants according to Pharmacogenomics Knowledge Base (PharmGKB) annotations identified 27 diplotypes and 26 variants with an evident clinical relevance. Comparison with global data illustrated a significant deviation of allele frequencies in the UAE population. Understudied populations display a distinct allelic architecture and various rare and unique variants. We underscored pharmacogenes with the highest variation frequencies and provided investigators with a list of candidate genes for future studies. Population pharmacogenomic studies are imperative during the pursuit of global pharmacogenomics implementation.
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Affiliation(s)
- Zeina N Al-Mahayri
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates
| | - George P Patrinos
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates.,Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, Patras, Greece.,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Sukanya Wattanapokayakit
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Nareenart Iemwimangsa
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Koya Fukunaga
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates. .,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates. .,Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
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10
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Verma S, Sharma I, Sharma V, Bhat A, Shah R, Bhat GR, Sharma B, Bakshi D, Nagpal A, Wakhloo A, Bhat A, Kumar R. MassArray analysis of genomic susceptibility variants in ovarian cancer. Sci Rep 2020; 10:21101. [PMID: 33273524 PMCID: PMC7713113 DOI: 10.1038/s41598-020-76491-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/28/2020] [Indexed: 12/24/2022] Open
Abstract
Ovarian cancer (OC), a multifaceted and genetically heterogeneous malignancy is one of the most common cancers among women. The aim of the study is to unravel the genetic factors associated with OC and the extent of genetic heterogeneity in the populations of Jammu and Kashmir (J&K).Using the high throughput Agena MassARRAY platform, present case control study was designed which comprises 200 histopathological confirmed OC patients and 400 age and ethnicity matched healthy controls to ascertain the association of previously reported eleven single nucleotide polymorphisms (SNPs) spread over ten genes (DNMT3A, PIK3CA, FGFR2, GSTP1, ERCC5, AKT1, CASC16, CYP19A1, BCL2 and ERCC1) within the OC population of Jammu and Kashmir, India. The association of each variant was estimated using logistic regression analyses. Out of the 11 SNPs the odds ratio observed for three SNPs; rs2699887 was (1.72 at 95% CI: 1.19-2.48, p = 0.004), rs1695 was (1.87 at 95% CI: 1.28-2.71, p = 0.001), and rs2298881 was (0.66 at 95% CI: 0.46-0.96, p = 0.03) were found significantly associated with the OC after correction with confounding factors i.e. age & BMI. Furthermore, the estimation of interactive analyses was performed and odds ratio observed was 2.44 (1.72-3.47), p value < 0. 001 suggests that there was a strong existence of interplay between the selected genetic variants in OC, which demonstrate that interactive analysis highlights the role of gene-gene interaction that provides an insight among multiple little effects of various polymorphisms in OC.
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Affiliation(s)
- Sonali Verma
- Indian Council of Medical Research-Centre for Advance Research, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Indu Sharma
- Ancient DNA Laboratory, Birbal Shani Institute of Paleo Sciences, Lucknow, Uttar Pradesh, India
| | - Varun Sharma
- Ancient DNA Laboratory, Birbal Shani Institute of Paleo Sciences, Lucknow, Uttar Pradesh, India
| | - Amrita Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ruchi Shah
- Department of Biotechnology, Kashmir University, Srinagar, Jammu and Kashmir, India
| | - Gh Rasool Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Bhanu Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Divya Bakshi
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ashna Nagpal
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ajay Wakhloo
- Department of Obstetrics and Gynecology, Government Medical College, Jammu, Jammu and Kashmir, India
| | - Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu, Jammu and Kashmir, India
| | - Rakesh Kumar
- Indian Council of Medical Research-Centre for Advance Research, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
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Update on next generation sequencing of pharmacokinetics-related genes: Development of the PKseq panel, a platform for amplicon sequencing of drug-metabolizing enzyme and drug transporter genes. Drug Metab Pharmacokinet 2020; 37:100370. [PMID: 33508759 DOI: 10.1016/j.dmpk.2020.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/01/2020] [Accepted: 11/18/2020] [Indexed: 02/08/2023]
Abstract
Genetic variation in pharmacokinetics (PK)-related genes encoding drug metabolizing enzymes or drug transporters is one of the most practical pharmacogenetic biomarkers for the prediction or explanation of an individual's response to drugs. Many pharmacogenomic variations are identified using targeted, whole-exome, and whole-genome sequencing, and the number of known novel variations and alleles in PK-related genes is increasing. The high homology of sequences among PK-related genes is suspected to lead to potential read misalignment and genotyping errors when short-read sequencing was performed. Therefore, highly efficient and accurate next generation sequencing (NGS) platforms for the sequencing of PK-related genes are needed. We have developed PKseq, a targeted sequencing panel based on multiplex PCR, which targets the coding regions of 37 drug transporters, 30 cytochrome P450 isoforms, 10 UDP-glucuronosyltransferases, 5 flavin-containing monooxygenases, 4 glutathione S-transferases, 4 sulfotransferases, and 10 other genes. In this review, we describe the current NGS platforms for the sequencing of PK-related genes. The NGS platforms, including the PKseq panel, will be useful not only for the identification of all the variants of PK-related genes associated with adverse drug reactions and drug efficacy, but also for clinical sequencing to achieve pharmacogenomics-based stratified medicine.
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Fukunaga K, Yamashita Y, Yagisawa T. Copy number variations in BOLA-DQA2, BOLA-DQB, and BOLA-DQA5 show the genomic architecture and haplotype frequency of major histocompatibility complex class II genes in Holstein cows. HLA 2020; 96:601-609. [PMID: 33006253 DOI: 10.1111/tan.14086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/13/2020] [Accepted: 09/28/2020] [Indexed: 12/26/2022]
Abstract
Bovine major histocompatibility complex (MHC) class II region contains many genes. The bovine leukocyte antigen (BoLA)-DRB3 was reportedly associated with susceptibility of various phenotypes of infections including bovine leukemia virus-induced lymphoma. However, the association of the remaining genes with various phenotypes has not been clarified due to the complicated genomic structure of the MHC class II region. Thus, in this study, we elucidated the MHC class II genomic structure, including the novel alleles and copy number variations (CNVs). We determined the copy numbers of BOLA-DQA2 (DQA2), BOLA-DQB (DQB2), BOLA-DQA5 (DQA5), BLA-DQB (DQB1), LOC100848815 (DQA1), and BOLA-DRB3 (DRB3) in 127 unrelated Holstein cows by TaqMan copy number assay. The genomes were sequenced using target next-generation sequencing (NGS) based on multiplex polymerase chain reaction. Combining the results of the copy numbers and alleles, we identified the BoLA alleles directly without haplotype estimation. Pairwise linkage disequilibrium (LD) analysis between alleles and genes were performed. The CNVs of DQA2, DQB2, and DQA5 in Holstein cows were detected. The frequency of the whole gene deletion in DQA2, DQB2, and DQA5 was 35.4%, 93.7%, and 93.7%, respectively. After target NGS, we identified 37 alleles in the six genes. Fifteen novel alleles (40.5%) were not registered in the IPD-MHC Database. LD analysis showed strong LD among the DQB2*deletion, DQA5*deletion, and DRB3*27:03 alleles. Our findings will provide important insights into the identification of the BoLA genes associated with various infection-related phenotypes.
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Affiliation(s)
- Koya Fukunaga
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yusuke Yamashita
- Hokkaido Chuo Agricultural Mutual Aid Association, Hokkaido, Japan
| | - Takuya Yagisawa
- Hokkaido Chuo Agricultural Mutual Aid Association, Hokkaido, Japan
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Determination of novel CYP2D6 haplotype using the targeted sequencing followed by the long-read sequencing and the functional characterization in the Japanese population. J Hum Genet 2020; 66:139-149. [PMID: 32759992 DOI: 10.1038/s10038-020-0815-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/08/2020] [Accepted: 07/26/2020] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing (NGS) has identified variations in cytochrome P450 (CYP) 2D6 associated with drug responses. However, determination of novel haplotypes is difficult because of the short reads generated by NGS. We aimed to identify novel CYP2D6 variants in the Japanese population and predict the CYP2D6 phenotype based on in vitro metabolic studies. Using a targeted NGS panel (PKSeq), 990 Japanese genomes were sequenced, and then novel CYP2D6 haplotypes were determined. Km, Vmax, and intrinsic clearance (Vmax/Km) of N-desmethyl-tamoxifen 4-hydroxylation were calculated by in vitro metabolic studies using cDNA-expressed CYP2D6 proteins. After determination of the CYP2D6 diplotypes, phenotypes of the individuals were predicted based on the in vitro metabolic activities. Targeted NGS identified 14 CYP2D6 variants not registered in the Pharmacogene Variation Consortium (PharmVar) database. Ten novel haplotypes were registered as CYP2D6*128 to *137 alleles in the PharmVar database. Based on the Vmax/Km value of each allele, *128, *129, *130, *131, *132, and *133 were predicted to be nonfunctional alleles. According to the results of the present study, six normal metabolizers (NM) and one intermediate (IM) metabolizers were designated as IM and poor metabolizers (PM), respectively. Our findings provide important insights into novel haplotypes and haplotypes of CYP2D6 and the effects on in vitro metabolic activities.
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Liblab S, Vusuratana A, Areepium N. ERCC1, XRCC1, and GSTP1 Polymorphisms and Treatment Outcomes of Advanced Epithelial Ovarian Cancer Patients Treated with Platinum-based Chemotherapy. Asian Pac J Cancer Prev 2020; 21:1925-1929. [PMID: 32711417 PMCID: PMC7573419 DOI: 10.31557/apjcp.2020.21.7.1925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Indexed: 12/04/2022] Open
Abstract
Objective: The first line regimen for treating epithelial ovarian cancer (EOC) is platinum-based chemotherapy. Various factors impact its effectiveness including polymorphisms of enzymes in platinum-related metabolism processes. Methods: We conducted the study to investigate the association between polymorphisms of ERCC1, XRCC1 and GSTP1, which responsible for platinum’s metabolisms in Thai epithelial ovarian cancer patients. Results: Fifty-two patients with advanced epithelial ovarian cancer were enrolled into this study. Genotyping analysis of ERCC1 (C->A, rs3212986), XRCC1 (A->G, rs25487) and GSTP (A->G, rs1695) were performed which variant allele frequencies were found at 35.6%, 28.9% and 10.6%, respectively. Patients with homozygous variant type (A/A) of ERCC1 C8092A had higher rate of platinum-resistance (75% vs 16.7%, p =0.046). In addition, the significant association of GSTP1 polymorphism and grade 2 anemia was found. Patients with A/G genotype of GSTP1 had higher rate of grade 2 anemia (81.8% vs 46.3%, p =0.036). Conclusions: Genetic polymorphisms of ERCC1, and GSTP1 might be useful biomarkers for prediction of clinical benefit and toxicities of platinum-based chemotherapy in Thai epithelial ovarian cancer patients.
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Affiliation(s)
- Salisa Liblab
- Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Apichai Vusuratana
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nutthada Areepium
- Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
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15
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Nakamura R, Ozeki T, Hirayama N, Sekine A, Yamashita T, Mashimo Y, Mizukawa Y, Shiohara T, Watanabe H, Sueki H, Ogawa K, Asada H, Kaniwa N, Tsukagoshi E, Matsunaga K, Niihara H, Yamaguchi Y, Aihara M, Mushiroda T, Saito Y, Morita E. Association of HLA-A*11:01 with Sulfonamide-Related Severe Cutaneous Adverse Reactions in Japanese Patients. J Invest Dermatol 2020; 140:1659-1662.e6. [PMID: 31981579 DOI: 10.1016/j.jid.2019.12.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 12/03/2019] [Accepted: 12/28/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Ryosuke Nakamura
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Japan
| | - Takeshi Ozeki
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Noriaki Hirayama
- Institute of Advanced Biosciences, Tokai University, Kanagawa, Japan
| | - Akihiro Sekine
- Center for Preventive Medical Science, Chiba University, Chiba, Japan
| | - Taiki Yamashita
- Center for Preventive Medical Science, Chiba University, Chiba, Japan
| | - Yoichi Mashimo
- Center for Preventive Medical Science, Chiba University, Chiba, Japan
| | - Yoshiko Mizukawa
- Department of Dermatology, Kyorin University School of Medicine, Tokyo, Japan
| | - Tetsuo Shiohara
- Department of Dermatology, Kyorin University School of Medicine, Tokyo, Japan
| | - Hideaki Watanabe
- Department of Dermatology, Showa University School of Medicine, Tokyo, Japan
| | - Hirohiko Sueki
- Department of Dermatology, Showa University School of Medicine, Tokyo, Japan
| | - Kohei Ogawa
- Department of Dermatology, Nara Medical University, Nara, Japan
| | - Hideo Asada
- Department of Dermatology, Nara Medical University, Nara, Japan
| | - Nahoko Kaniwa
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Japan
| | - Eri Tsukagoshi
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Japan
| | - Kayoko Matsunaga
- Department of Integrative Medical Science for Allergic Disease, Fujita Health University School of Medicine, Aichi, Japan
| | - Hiroyuki Niihara
- Department of Dermatology, Shimane University Faculty of Medicine, Shimane, Japan
| | - Yukie Yamaguchi
- Department of Environmental Immuno-Dermatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Michiko Aihara
- Department of Environmental Immuno-Dermatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshiro Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Japan.
| | - Eishin Morita
- Department of Dermatology, Shimane University Faculty of Medicine, Shimane, Japan
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Chumnumwat S, Lu ZH, Sukasem C, Winther MD, Capule FR, Abdul Hamid AAAT, Bhandari B, Chaikledkaew U, Chanhom N, Chantarangsu S, Charoenyingwattana A, Hang TT, Hlaing TM, Htun KS, Jittikoon J, Le L, Mahasirimongkol S, Mohamed Noor DA, Shrestha J, Suwannoi L, Tragulpiankit P, Turongkaravee S, Wattanapokayakit S, Xangsayarath P, Yuliwulandari R, Zain SM, Chantratita W. Southeast Asian Pharmacogenomics Research Network (SEAPharm): Current Status and Perspectives. Public Health Genomics 2019; 22:132-139. [PMID: 31587001 DOI: 10.1159/000502916] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 08/25/2019] [Indexed: 11/19/2022] Open
Abstract
Pharmacogenomics (PGx) is increasingly being recognized as a potential tool for improving the efficacy and safety of drug therapy. Therefore, several efforts have been undertaken globally to facilitate the implementation process of PGx into routine clinical practice. Part of these efforts include the formation of PGx working groups working on PGx research, synthesis, and dissemination of PGx data and creation of PGx implementation strategies. In Asia, the Southeast Asian Pharmacogenomics Research Network (SEAPharm) is established to enable and strengthen PGx research among the various PGx communities within but not limited to countries in SEA; with the ultimate goal to support PGx implementation in the region. From the perspective of SEAPharm member countries, there are several key elements essential for PGx implementation at the national level. They include pharmacovigilance database, PGx research, health economics research, dedicated laboratory to support PGx testing for both research and clinical use, structured PGx education, and supportive national health policy. The status of these essential elements is presented here to provide a broad picture of the readiness for PGx implementation among the SEAPharm member countries, and to strengthen the PGx research network and practice in this region.
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Affiliation(s)
- Supatat Chumnumwat
- Department of Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Zen Huat Lu
- PAPRSB Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei Darussalam
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Michael David Winther
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Francis R Capule
- Department of Pharmacy, College of Pharmacy, University of the Philippines, Manila, Philippines
| | | | - Bibek Bhandari
- Kathmandu Medical College Teaching Hospital, Kathmandu, Nepal
| | - Usa Chaikledkaew
- Department of Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Noppadol Chanhom
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Soranun Chantarangsu
- Department of Oral Pathology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Angkana Charoenyingwattana
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Tong Thi Hang
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Tin Maung Hlaing
- Defence Services Medical Research Centre (DSMRC), Nay Pyi Taw, Myanmar/Burma
| | - Kyaw Soe Htun
- Defence Services Medical Research Centre (DSMRC), Nay Pyi Taw, Myanmar/Burma
| | - Jiraphun Jittikoon
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam.,Vingroup Big Data Institute, Hanoi, Vietnam
| | - Surakameth Mahasirimongkol
- Department of Medical Sciences, Medical Genetics Center, Medical Life Sciences Institute, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Jesus Shrestha
- Kathmandu Medical College Teaching Hospital, Kathmandu, Nepal
| | - Lakkana Suwannoi
- Department of Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | | | | | - Sukanya Wattanapokayakit
- Department of Medical Sciences, Medical Genetics Center, Medical Life Sciences Institute, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Rika Yuliwulandari
- Department of Pharmacology, Faculty of Medicine, YARSI University, Jakarta, Indonesia
| | - Shamsul Mohd Zain
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand,
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