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Pharmacogenomics: Precision Medicine and Drug Response
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Pharmacogenomics: Precision Medicine and Drug Response

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (10 January 2022) | Viewed by 24355

Special Issue Editor

Dr. Emiliano Giardina

E-Mail Website
Guest Editor
1. Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, 00142 Rome, Italy
2. Forensic Genetics Laboratoty, Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
Interests: forensic genetics; genetic counselling; human identification; neurogenetics; prenatal and postnatal genetic diagnosis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The advances in disease treatment have allowed the development of new therapeutic approaches. Over the years, many therapies have shown different efficacy profiles, supporting the development of precision medicine. Several pharmacogenomic approaches have been used to individualize treatments, optimizing dosage and preventing adverse effects. With the recent development of new high-throughput technologies and massive parallel sequencing, it is now possible to test the entire human genome to reveal positive associations between specific variations and the response to drugs in terms of efficacy and safety. Although numerous associations have been published, the translation to clinical practice in some areas has been minimal. A notable exception to this is the oncological field.

This Special Issue aims to curate available practical information in the pharmacogenomic domain to promote the translation of research data into precision medical protocols. Particular attention will be paid to new bioinformatic approaches to the interpretation of omic data and to research advances in populations that up to this point have little study data. At the same time, drug repurposing approaches will be encouraged to promote alternative applications of drugs with existing approval for use. This Special Issue of Genes will highlight recent advances in the field, and innovations in the use of omic data in the treatment of human diseases. Clinical and molecular studies, as well as reviews, will be considered for publication in this Issue. 

Prof. Dr. Emiliano Giardina
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Pharmacogenomics
  • Drug Repurposing
  • Precision Medicine
  • Drug response
  • Personalized therapies

Published Papers (7 papers)

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Editorial

Jump to: Research, Review

3 pages, 191 KiB  
Editorial
The Future of Pharmacogenomics Requires New Discoveries and Innovative Education
by Emiliano Giardina and Stefania Zampatti
Genes 2022, 13(9), 1575; https://doi.org/10.3390/genes13091575 - 02 Sep 2022
Viewed by 1599
Abstract
Since the beginning of pharmacology, several variations in responses to drugs have been recorded [...] Full article
(This article belongs to the Special Issue Pharmacogenomics: Precision Medicine and Drug Response)

Research

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10 pages, 893 KiB  
Article
The Role of SLC22A1 and Genomic Ancestry on Toxicity during Treatment in Children with Acute Lymphoblastic Leukemia of the Amazon Region
by Sweny de S. M. Fernandes, Luciana P. C. Leitão, Amanda de N. Cohen-Paes, Laura P. A. Gellen, Lucas F. Pastana, Darlen C. de Carvalho, Antônio A. C. Modesto, Ana C. A. da Costa, Alayde V. Wanderley, Carlos H. V. de Lima, Esdras E. B. Pereira, Marianne R. Fernandes, Rommel M. R. Burbano, Paulo P. de Assumpção, Sidney E. B. dos Santos and Ney P. C. dos Santos
Genes 2022, 13(4), 610; https://doi.org/10.3390/genes13040610 - 29 Mar 2022
Cited by 3 | Viewed by 2058
Abstract
In Brazil, Acute lymphoid leukemia (ALL) is the leading cause of cancer deaths in children and adolescents. Treatment toxicity is one of the reasons for stopping chemotherapy. Amerindian genomic ancestry is an important factor for this event due to fluctuations in frequencies of [...] Read more.
In Brazil, Acute lymphoid leukemia (ALL) is the leading cause of cancer deaths in children and adolescents. Treatment toxicity is one of the reasons for stopping chemotherapy. Amerindian genomic ancestry is an important factor for this event due to fluctuations in frequencies of genetic variants, as in the NUDT15 and SLC22A1 genes, which make up the pharmacokinetic and pharmacodynamic pathways of chemotherapy. This study aimed to investigate possible associations between NUDT15 (rs1272632214) and SLC22A1 (rs202220802) gene polymorphism and genomic ancestry as a risk of treatment toxicities in patients with childhood ALL in the Amazon region of Brazil. The studied population consisted of 51 patients with a recent diagnosis of ALL when experiencing induction therapy relative to the BFM 2009 protocol. Our results evidenced a significant association of risk of severe infectious toxicity for the variant of the SLC22A1 gene (OR: 3.18, p = 0.031). Genetic ancestry analyses demonstrated that patients who had a high contribution of African ancestry had a significant protective effect for the development of toxicity (OR: 0.174; p = 0.010), possibly due to risk effects of the Amerindian contribution. Our results indicate that mixed populations with a high degree of African ancestry have a lower risk of developing general toxicity during induction therapy for ALL. In addition, individuals with the SLC22A1 variant have a higher risk of developing severe infectious toxicity while undergoing the same therapy. Full article
(This article belongs to the Special Issue Pharmacogenomics: Precision Medicine and Drug Response)
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10 pages, 498 KiB  
Article
Impact of Variants in the ATIC and ARID5B Genes on Therapeutic Failure with Imatinib in Patients with Chronic Myeloid Leukemia
by Karla Beatriz Cardias Cereja Pantoja, Tereza Cristina de Brito Azevedo, Darlen Cardoso de Carvalho, Natasha Monte, Amanda de Nazaré Cohen Paes, Maria Clara da Costa Barros, Lui Wallacy Morikawa Souza Vinagre, Ana Rosa Sales de Freitas, Rommel Mario Rodríguez Burbano, Paulo Pimentel de Assumpção, Sidney Emanuel Batista dos Santos, Marianne Rodrigues Fernandes and Ney Pereira Carneiro dos Santos
Genes 2022, 13(2), 330; https://doi.org/10.3390/genes13020330 - 10 Feb 2022
Cited by 4 | Viewed by 2146
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm derived from the balanced reciprocal translocation of chromosomes 9 and 22 t (9q34 and 22q11), which leads to the formation of the Philadelphia chromosome and fusion of the BCR-ABL genes. The first-line treatment for CML [...] Read more.
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm derived from the balanced reciprocal translocation of chromosomes 9 and 22 t (9q34 and 22q11), which leads to the formation of the Philadelphia chromosome and fusion of the BCR-ABL genes. The first-line treatment for CML is imatinib, a tyrosine kinase inhibitor that acts on the BCR-ABL protein. However, even though it is a target-specific drug, about 25% of patients do not respond to this treatment. The resistance mechanisms involved in this process have been investigated and studies have shown that germinal alterations can influence this mechanism. The aim of this work was to investigate 32 polymorphisms in 24 genes of carcinogenic pathway to verify the influence of these genetic variants on the response to treatment with imatinib. Our results demonstrated that individuals with the recessive GG genotype for the rs2372536 variant in the ATIC gene are approximately three times more likely to experience treatment failure with imatinib (p = 0.045, HR = 2.726, 95% CI = 0.9986–7.441), as well as individuals with the TT genotype for the rs10821936 variant in the ARID5B gene, who also have a higher risk for treatment failure with imatinib over time (p = 0.02, HR = 0.4053, IC 95% = 0.1802–0.911). In conclusion, we show that variants in the ATIC and ARIDB5 gene, never screened in previous studies, could potentially influence the therapeutic response to imatinib in patients treated for CML. Full article
(This article belongs to the Special Issue Pharmacogenomics: Precision Medicine and Drug Response)
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8 pages, 1834 KiB  
Article
Tumor-Associated Macrophage Promotes the Survival of Cancer Cells upon Docetaxel Chemotherapy via the CSF1/CSF1R–CXCL12/CXCR4 Axis in Castration-Resistant Prostate Cancer
by Wei Guan, Fan Li, Zhenyu Zhao, Zongbiao Zhang, Junhui Hu and Yan Zhang
Genes 2021, 12(5), 773; https://doi.org/10.3390/genes12050773 - 19 May 2021
Cited by 30 | Viewed by 3026
Abstract
Castration-resistant prostate cancer (CRPC) is an advanced stage of prostate cancer that can progress rapidly even in patients treated with castration. Previously, we found that tumor-associated macrophages (TAM) can be recruited by CSF-1 secreted by docetaxel-treated prostate cancer cells and promote the survival [...] Read more.
Castration-resistant prostate cancer (CRPC) is an advanced stage of prostate cancer that can progress rapidly even in patients treated with castration. Previously, we found that tumor-associated macrophages (TAM) can be recruited by CSF-1 secreted by docetaxel-treated prostate cancer cells and promote the survival of cancer cells in response to chemotherapy. The inhibition of CSF-1R can impede this effect and significantly prolong survival in xenograft mice. However, the actual mechanism of how TAM improves cancer cell survival still remains elusive and controversial. Here, for the first time, we found that the enhanced survival of cancer cells achieved by TAM was mainly mediated by CXCR4 activation from the increased secretion of CXCL12 from CSF-1 activated TAM. This finding helps to clarify the mechanism of chemoresistance for second-line chemotherapy using docetaxel, facilitating the development of novel drugs to overcome immune tolerance in castration-resistant prostate cancer. Full article
(This article belongs to the Special Issue Pharmacogenomics: Precision Medicine and Drug Response)
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Review

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31 pages, 486 KiB  
Review
Pharmacogenetics of Drugs Used in the Treatment of Cancers
by Beata Franczyk, Jacek Rysz and Anna Gluba-Brzózka
Genes 2022, 13(2), 311; https://doi.org/10.3390/genes13020311 - 07 Feb 2022
Cited by 10 | Viewed by 7714
Abstract
Pharmacogenomics is based on the understanding of the individual differences in drug use, the response to drug therapy (efficacy and toxicity), and the mechanisms underlying variable drug responses. The identification of DNA variants which markedly contribute to inter-individual variations in drug responses would [...] Read more.
Pharmacogenomics is based on the understanding of the individual differences in drug use, the response to drug therapy (efficacy and toxicity), and the mechanisms underlying variable drug responses. The identification of DNA variants which markedly contribute to inter-individual variations in drug responses would improve the efficacy of treatments and decrease the rate of the adverse side effects of drugs. This review focuses only on the impact of polymorphisms within drug-metabolizing enzymes on drug responses. Anticancer drugs usually have a very narrow therapeutic index; therefore, it is very important to use appropriate doses in order to achieve the maximum benefits without putting the patient at risk of life-threatening toxicities. However, the adjustment of the appropriate dose is not so easy, due to the inheritance of specific polymorphisms in the genes encoding the target proteins and drug-metabolizing enzymes. This review presents just a few examples of such polymorphisms and their impact on the response to therapy. Full article
(This article belongs to the Special Issue Pharmacogenomics: Precision Medicine and Drug Response)
19 pages, 402 KiB  
Review
Role of Actionable Genes in Pursuing a True Approach of Precision Medicine in Monogenic Diabetes
by Antonella Marucci, Irene Rutigliano, Grazia Fini, Serena Pezzilli, Claudia Menzaghi, Rosa Di Paola and Vincenzo Trischitta
Genes 2022, 13(1), 117; https://doi.org/10.3390/genes13010117 - 09 Jan 2022
Cited by 9 | Viewed by 3040
Abstract
Monogenic diabetes is a genetic disorder caused by one or more variations in a single gene. It encompasses a broad spectrum of heterogeneous conditions, including neonatal diabetes, maturity onset diabetes of the young (MODY) and syndromic diabetes, affecting 1–5% of patients with diabetes. [...] Read more.
Monogenic diabetes is a genetic disorder caused by one or more variations in a single gene. It encompasses a broad spectrum of heterogeneous conditions, including neonatal diabetes, maturity onset diabetes of the young (MODY) and syndromic diabetes, affecting 1–5% of patients with diabetes. Some of these variants are harbored by genes whose altered function can be tackled by specific actions (“actionable genes”). In suspected patients, molecular diagnosis allows the implementation of effective approaches of precision medicine so as to allow individual interventions aimed to prevent, mitigate or delay clinical outcomes. This review will almost exclusively concentrate on the clinical strategy that can be specifically pursued in carriers of mutations in “actionable genes”, including ABCC8, KCNJ11, GCK, HNF1A, HNF4A, HNF1B, PPARG, GATA4 and GATA6. For each of them we will provide a short background on what is known about gene function and dysfunction. Then, we will discuss how the identification of their mutations in individuals with this form of diabetes, can be used in daily clinical practice to implement specific monitoring and treatments. We hope this article will help clinical diabetologists carefully consider who of their patients deserves timely genetic testing for monogenic diabetes. Full article
(This article belongs to the Special Issue Pharmacogenomics: Precision Medicine and Drug Response)
13 pages, 269 KiB  
Review
Pharmacogenomics: An Update on Biologics and Small-Molecule Drugs in the Treatment of Psoriasis
by Valerio Caputo, Claudia Strafella, Terenzio Cosio, Caterina Lanna, Elena Campione, Giuseppe Novelli, Emiliano Giardina and Raffaella Cascella
Genes 2021, 12(9), 1398; https://doi.org/10.3390/genes12091398 - 10 Sep 2021
Cited by 27 | Viewed by 3688
Abstract
Pharmacogenomic studies allowed the reasons behind the different responses to treatments to be understood. Its clinical utility, in fact, is demonstrated by the reduction in adverse drug reaction incidence and the improvement of drug efficacy. Pharmacogenomics is an important tool that is able [...] Read more.
Pharmacogenomic studies allowed the reasons behind the different responses to treatments to be understood. Its clinical utility, in fact, is demonstrated by the reduction in adverse drug reaction incidence and the improvement of drug efficacy. Pharmacogenomics is an important tool that is able to improve the drug therapy of different disorders. In particular, this review will highlight the current pharmacogenomics knowledge about biologics and small-molecule treatments for psoriasis. To date, studies performed on genes involved in the metabolism of biological drugs (tumor necrosis factor inhibitors and cytokines inhibitors) and small molecules (apremilast, dimethyl fumarate, and tofacitinib) have provided conflicting results, and further investigations are necessary in order to establish a set of biomarkers to be introduced into clinical practice. Full article
(This article belongs to the Special Issue Pharmacogenomics: Precision Medicine and Drug Response)
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