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Pharmacogenomics, 3rd Edition
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Pharmacogenomics, 3rd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pharmacology".

Deadline for manuscript submissions: closed (20 September 2024) | Viewed by 12609

Special Issue Editor

Prof. Dr. Ramón Cacabelos

E-Mail Website
Guest Editor
Euroespes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Corunna, Spain
Interests: pharmacogenomics; pharmacoepigenetics; genomics of brain disorders; neuroepigenetics; CNS drug development; neurodegenerative disorders; Alzheimer’s disease; Parkinson’s disease
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is a great pleasure for me to accept the kind invitation of the International Journal of Molecular Sciences to serve as Guest Editor of a Special Issue on “Pharmacogenomics”. I think that this is a timely initiative which will be of interest to most medical disciplines. Cardiovascular disorders (25%–30%), cancer (20%–25%) and brain disorders (10%–15%) represent over 60%–70% of morbility and mortality in developed countries. Approximately 10%–20% of direct costs for disease management are attributed to pharmacological treatment, and, unfortunately, it is estimated that drug efficacy is restricted to 20%–30% of the cases treated with a particular drug in almost any medical specialty. Many different factors influence drug efficacy and safety, including the chemical properties of a drug, route of administration, disease stage, nutrition, compliance, drug–drug interactions, and pharmacogenomics.

In the coming years, the onset of a revolutionary transformation of protocols and strategies for drug development is expected. Pharmacogenomics is one of the doors through which to enter the complex building of personalized medicine.

Regulatory agencies should make recommendations to the pharmaceutical industry in favor of the introduction of pharmacogenomics in drug development and the inclusion of pharmacogenomic information on drug labels, with specific warnings for the population at risk. Educational programs are fundamental for drug prescribers to become familiar with personalized treatments. Pharmacogenetic testing should be gradually introduced into medical practice. The introduction of pharmacogenomics in routine clinical practice is fundamental for optimizing therapeutics and for reducing adverse drug reactions (ADRs), which are a major health concern worldwide. There are multiple causes of ADRs, some of which are preventable. Pharmacogenomics accounts for ≈80% of the variability in drug efficacy and safety. Over 400 genes are clinically relevant in drug metabolism, and ≈200 pharmagenes are associated with ADRs. The condition of extensive metabolizers in the Caucasian population is lower than 20%, and about 60% of patients are exposed to potential ADRs.

I would like to invite all of you, experts and beginners in the field of pharmacogeneomics, to contribute to this Special Issue with your ideas for accelerating the implementation of pharmacogenomic procedures in drug development and clinical practice.

More published papers could be found in the closed Special Issue: Pharmacogenomics and Pharmacogenomics 2.0.

Prof. Dr. Ramón Cacabelos
Guest Editor

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • pharmacogenomics of cardiovascular disorders
  • pharmacogenomics of cancer
  • pharmacogenomics of brain disorders
  • pharmacogenomics of metabolic and endocrine disorders
  • pharmacogenomics of gastrointestinal disorders
  • pharmacogenomics of lipid metabolism disorders
  • pharmacoepigenomics of pain
  • pharmacogenomics of psychotropic drugs
  • neurodegenerative disorders (Alzheimer, Parkinson, multiple sclerosis)

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Published Papers (6 papers)

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Research

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19 pages, 1408 KiB  
Article
A Comparison of Molecular Techniques for Improving the Methodology in the Laboratory of Pharmacogenetics
by María Celsa Peña-Martín, Elena Marcos-Vadillo, Belén García-Berrocal, David Hansoe Heredero-Jung, María Jesús García-Salgado, Sandra Milagros Lorenzo-Hernández, Romain Larrue, Marie Lenski, Guillaume Drevin, Catalina Sanz and María Isidoro-García
Int. J. Mol. Sci. 2024, 25(21), 11505; https://doi.org/10.3390/ijms252111505 - 26 Oct 2024
Viewed by 1392
Abstract
One of the most critical goals in healthcare is safe and effective drug therapy, which is directly related to an individual’s response to treatment. Precision medicine can improve drug safety in many scenarios, including polypharmacy, and it requires the development of new genetic [...] Read more.
One of the most critical goals in healthcare is safe and effective drug therapy, which is directly related to an individual’s response to treatment. Precision medicine can improve drug safety in many scenarios, including polypharmacy, and it requires the development of new genetic characterization methods. In this report, we use real-time PCR, microarray techniques, and mass spectrometry (MALDI-TOF), which allows us to compare them and identify the potential benefits of technological improvements, leading to better quality medical care. These comparative studies, as part of our pharmacogenetic Five-Step Precision Medicine (5SPM) approach, reveal the superiority of mass spectrometry over the other methods analyzed and highlight the importance of updating the laboratory’s pharmacogenetic methodology to identify new variants with clinical impact. Full article
(This article belongs to the Special Issue Pharmacogenomics, 3rd Edition)
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12 pages, 1070 KiB  
Article
CYP3A4*1B but Not CYP3A5*3 as Determinant of Long-Term Tacrolimus Dose Requirements in Spanish Solid Organ Transplant Patients
by Julia Concha, Estela Sangüesa, María Pilar Ribate and Cristina B. García
Int. J. Mol. Sci. 2024, 25(20), 11327; https://doi.org/10.3390/ijms252011327 - 21 Oct 2024
Viewed by 1666
Abstract
Tacrolimus (TAC) is a commonly used immunosuppressive drug in solid organ transplantation. Pharmacogenetics has been demonstrated before to be decisive in TAC pharmacotherapy. The CYP3A5*3 variant has been reported to be the main determinant of TAC dose requirements; however, other polymorphisms have also [...] Read more.
Tacrolimus (TAC) is a commonly used immunosuppressive drug in solid organ transplantation. Pharmacogenetics has been demonstrated before to be decisive in TAC pharmacotherapy. The CYP3A5*3 variant has been reported to be the main determinant of TAC dose requirements; however, other polymorphisms have also proven to be influential, especially in CYP3A5 non-expressor patients. The aim of this study is to evaluate the influence of genetic polymorphisms in TAC therapy in a cohort of Spanish transplant recipients. Genetic analysis including ten polymorphic variants was performed, and demographic and clinical data and pharmacotherapy of 26 patients were analyzed. No significant differences were found in weight-adjusted dose between CYP3A5 expressors and non-expressors (0.047 mg/kg vs. 0.044 mg/kg), while they were found for carriers of the CYP3A4*1B allele (0.101 mg/kg; p < 0.05). The results showed that patients with at least one CYP3A4*1B allele had a higher TAC dose and lower blood concentration. Dose-adjusted TAC blood levels were also lower in CYP3A4*1B carriers compared to non-carriers (0.72 ng/mL/mg vs. 2.88 ng/mL/mg). These results support the independence of CYP3A5*3 and CYP3A4*1B variants as determinants of dose requirements despite the linkage disequilibrium present between the two. The variability in genotype frequency between ethnicities may be responsible for the discrepancy found between studies. Full article
(This article belongs to the Special Issue Pharmacogenomics, 3rd Edition)
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12 pages, 733 KiB  
Article
An Inexpensive and Quick Method for Genotyping of HLA Variants Included in the Spanish Pharmacogenomic Portfolio of National Health System
by Irene Taladriz-Sender, Gina Hernández-Osio, Paula Zapata-Cobo, Sara Salvador-Martín, Xandra García-González, Antonio Balas, María Sanjurjo-Sáez and Luis A. López-Fernández
Int. J. Mol. Sci. 2024, 25(20), 11207; https://doi.org/10.3390/ijms252011207 - 18 Oct 2024
Viewed by 1021
Abstract
The possibility of using the same genotyping technology (TaqMan) for all the genetic tests included in the new Spanish pharmacogenomics portfolio should enable the application of a multigenotyping platform to obtain a whole pharmacogenomics profile. However, HLA-typing is usually performed with other technologies [...] Read more.
The possibility of using the same genotyping technology (TaqMan) for all the genetic tests included in the new Spanish pharmacogenomics portfolio should enable the application of a multigenotyping platform to obtain a whole pharmacogenomics profile. However, HLA-typing is usually performed with other technologies and needs to be adapted to TaqMan assays. Our aim was to establish a set of TaqMan assays for correct typing of HLA-A*31:01, HLA-B*15:02, HLA-B*57:01, and HLA-B*58:01. Therefore, we searched for and selected SNVs described in different populations as surrogate markers for these HLA alleles, designed TaqMan assays, and tested in a set of samples with known HLA-A and HLA-B. HLA-A*31:01 was correctly typed with a combination of rs1061235 and rs17179220 (PPV 100%, 95% CI 84.6–100-%; NPV 100%, 95% CI 96.5–100.0%), HLA-B*15:02 with rs10484555 (PPV 100%, 95% CI 69.2–100.0%; NPV 100%, 95% CI 96.8–100.0%) and rs144012689 (PPV 100%, 95% CI 69.2–100.0%; NPV 100%, 95% CI 96.8–100.0%), and HLA-B*57:01 with rs2395029 (PPV 99.5%, 95% CI 72.9–99.3%; NPV 99.5%, 95% CI 98.3–100.0%). HLA-B*58:01 was typed using two allele-specific TaqMan probes mixed with a ß-Globin reference and treated as a genotyping assay (PPV 100.0%, 95% CI 81.5–100.0%; NPV 100%, 95% CI 96.8–100.0%). In conclusion, we demonstrated a clinically useful way to type HLA-A and HLA-B alleles included in the Spanish pharmacogenomics portfolio using TaqMan assays. Full article
(This article belongs to the Special Issue Pharmacogenomics, 3rd Edition)
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14 pages, 2367 KiB  
Article
SLCO1B1 Exome Sequencing and Statin Treatment Response in 64,000 UK Biobank Patients
by Deniz Türkmen, Jack Bowden, Jane A. H. Masoli, David Melzer and Luke C. Pilling
Int. J. Mol. Sci. 2024, 25(8), 4426; https://doi.org/10.3390/ijms25084426 - 17 Apr 2024
Cited by 2 | Viewed by 2667
Abstract
The solute carrier organic anion transporter family member 1B1 (SLCO1B1) encodes the organic anion-transporting polypeptide 1B1 (OATP1B1 protein) that transports statins to liver cells. Common genetic variants in SLCO1B1, such as *5, cause altered systemic exposure to statins and therefore [...] Read more.
The solute carrier organic anion transporter family member 1B1 (SLCO1B1) encodes the organic anion-transporting polypeptide 1B1 (OATP1B1 protein) that transports statins to liver cells. Common genetic variants in SLCO1B1, such as *5, cause altered systemic exposure to statins and therefore affect statin outcomes, with potential pharmacogenetic applications; yet, evidence is inconclusive. We studied common and rare SLCO1B1 variants in up to 64,000 patients from UK Biobank prescribed simvastatin or atorvastatin, combining whole-exome sequencing data with up to 25-year routine clinical records. We studied 51 predicted gain/loss-of-function variants affecting OATP1B1. Both SLCO1B1*5 alone and the SLCO1B1*15 haplotype increased LDL during treatment (beta*5 = 0.08 mmol/L, p = 6 × 10−8; beta*15 = 0.03 mmol/L, p = 3 × 10−4), as did the likelihood of discontinuing statin prescriptions (hazard ratio*5 = 1.12, p = 0.04; HR*15 = 1.05, p = 0.04). SLCO1B1*15 and SLCO1B1*20 increased the risk of General Practice (GP)-diagnosed muscle symptoms (HR*15 = 1.22, p = 0.003; HR*20 = 1.25, p = 0.01). We estimated that genotype-guided prescribing could potentially prevent 18% and 10% of GP-diagnosed muscle symptoms experienced by statin patients, with *15 and *20, respectively. The remaining common variants were not individually significant. Rare variants in SLCO1B1 increased LDL in statin users by up to 1.05 mmol/L, but replication is needed. We conclude that genotype-guided treatment could reduce GP-diagnosed muscle symptoms in statin patients; incorporating further SLCO1B1 variants into clinical prediction scores could improve LDL control and decrease adverse events, including discontinuation. Full article
(This article belongs to the Special Issue Pharmacogenomics, 3rd Edition)
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11 pages, 694 KiB  
Article
Frequencies of Combined Dysfunction of Cytochromes P450 2C9, 2C19, and 2D6 in an Italian Cohort: Suggestions for a More Appropriate Medication Prescribing Process
by Giovanna Gentile, Ottavia De Luca, Antonio Del Casale, Gerardo Salerno, Maurizio Simmaco and Marina Borro
Int. J. Mol. Sci. 2023, 24(16), 12696; https://doi.org/10.3390/ijms241612696 - 11 Aug 2023
Cited by 1 | Viewed by 1224
Abstract
Improper drug prescription is a main cause of both drug-related harms (inefficacy and toxicity) and ineffective spending and waste of the healthcare system’s resources. Nowadays, strategies to support an improved, informed prescription process may benefit from the adequate use of pharmacogenomic testing. Using [...] Read more.
Improper drug prescription is a main cause of both drug-related harms (inefficacy and toxicity) and ineffective spending and waste of the healthcare system’s resources. Nowadays, strategies to support an improved, informed prescription process may benefit from the adequate use of pharmacogenomic testing. Using next-generation sequencing, we analyzed the genomic profile for three major cytochromes P450 (CYP2C9, CYP2C19, CYP2D6) and studied the frequencies of dysfunctional isozymes (e.g., poor, intermediate, or rapid/ultra-rapid metabolizers) in a cohort of 298 Italian subjects. We found just 14.8% of subjects with a fully normal set of cytochromes, whereas 26.5% of subjects had combined cytochrome dysfunction (more than one isozyme involved). As improper drug prescription is more frequent, and more burdening, in polytreated patients, since drug–drug interactions also cause patient harm, we discuss the potential benefits of a more comprehensive PGX testing approach to support informed drug selection in such patients. Full article
(This article belongs to the Special Issue Pharmacogenomics, 3rd Edition)
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Review

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19 pages, 1782 KiB  
Review
Receptor Pharmacogenomics: Deciphering Genetic Influence on Drug Response
by Sorina Andreea Anghel, Cristina-Elena Dinu-Pirvu, Mihaela-Andreea Costache, Ana Maria Voiculescu, Mihaela Violeta Ghica, Valentina Anuța and Lăcrămioara Popa
Int. J. Mol. Sci. 2024, 25(17), 9371; https://doi.org/10.3390/ijms25179371 - 29 Aug 2024
Cited by 2 | Viewed by 3757
Abstract
The paradigm “one drug fits all” or “one dose fits all” will soon be challenged by pharmacogenetics research and application. Drug response—efficacy or safety—depends on interindividual variability. The current clinical practice does not include genetic screening as a routine procedure and does not [...] Read more.
The paradigm “one drug fits all” or “one dose fits all” will soon be challenged by pharmacogenetics research and application. Drug response—efficacy or safety—depends on interindividual variability. The current clinical practice does not include genetic screening as a routine procedure and does not account for genetic variation. Patients with the same illness receive the same treatment, yielding different responses. Integrating pharmacogenomics in therapy would provide critical information about how a patient will respond to a certain drug. Worldwide, great efforts are being made to achieve a personalized therapy-based approach. Nevertheless, a global harmonized guideline is still needed. Plasma membrane proteins, like receptor tyrosine kinase (RTK) and G protein-coupled receptors (GPCRs), are ubiquitously expressed, being involved in a diverse array of physiopathological processes. Over 30% of drugs approved by the FDA target GPCRs, reflecting the importance of assessing the genetic variability among individuals who are treated with these drugs. Pharmacogenomics of transmembrane protein receptors is a dynamic field with profound implications for precision medicine. Understanding genetic variations in these receptors provides a framework for optimizing drug therapies, minimizing adverse reactions, and advancing the paradigm of personalized healthcare. Full article
(This article belongs to the Special Issue Pharmacogenomics, 3rd Edition)
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