Pharmacogenetics and Genomic Biomarkers and Their Application in Clinical Practice

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Biopharmaceuticals".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 21140

Special Issue Editor

UniCamillus- Saint Camillus International University of Health Sciences, Rome, Italy
Interests: genetics of complex diseases; pharmacogenetics; microRNA; genetic variability
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent decades, genetic information has acquired an increasing importance not only in the understanding of diseases’ pathogenesis but also in the prediction of diseases’ prognosis and treatment. We know that each individual is different and each patient has a personal genetic background that could be involved in the modulation of the clinical phenotype and with a different response to a drug treatment. Therefore, the identification and qualification of genomic biomarkers able to better monitor the disease course or predict the outcome of a treatment are crucial in clinical practice. In specific fields, such as in oncology, the genetic characterization of tumor tissue is already applied, and it is a standard approach to choose a specific and personalized therapy for each patient. Some applications in clinical practice are already available also to prevent the appearance of adverse drug reactions; for example, with simple genetic testing before drug administration, such as HLA genotyping, it is possible to avoid Abacavir hypersensitivity. Therefore, this Special Issue on “Pharmacogenetics and Genomic Biomarkers and their Application in Clinical Practice” will include both regular articles and reviews focused on how genes influence an individual’s response to pharmacotherapy and on genomics biomarkers most promising to be applied in clinical practice to more precisely diagnose disease and prescribe specific treatments.

Dr. Cinzia Ciccacci
Guest Editor

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Keywords

  • Genomic biomarkers
  • Pharmacogenomics
  • Pharmacogenetics
  • Predictive medicine
  • Personalized therapy
  • Genetics and drug response

Published Papers (5 papers)

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Research

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19 pages, 2760 KiB  
Article
Integration of Transcriptome and Exome Genotyping Identifies Significant Variants with Autism Spectrum Disorder
by Noor B. Almandil, Abdulla AlSulaiman, Sumayh A. Aldakeel, Deem N. Alkuroud, Halah Egal Aljofi, Safah Alzahrani, Aishah Al-mana, Asma A. Alfuraih, Majed Alabdali, Fahd A. Alkhamis, Sayed AbdulAzeez and J. Francis Borgio
Pharmaceuticals 2022, 15(2), 158; https://0-doi-org.brum.beds.ac.uk/10.3390/ph15020158 - 27 Jan 2022
Cited by 3 | Viewed by 3236
Abstract
Autism is a complex disease with genetic predisposition factors. Real factors for treatment and early diagnosis are yet to be defined. This study integrated transcriptome and exome genotyping for identifying functional variants associated with autism spectrum disorder and their impact on gene expression [...] Read more.
Autism is a complex disease with genetic predisposition factors. Real factors for treatment and early diagnosis are yet to be defined. This study integrated transcriptome and exome genotyping for identifying functional variants associated with autism spectrum disorder and their impact on gene expression to find significant variations. More than 1800 patients were screened, and 70 (47 male/23 female) with an average age of 7.56 ± 3.68 years fulfilled the DSM-5 criteria for autism. Analysis revealed 682 SNPs of 589 genes significantly (p < 0.001) associated with autism among the putative functional exonic variants (n = 243,345) studied. Olfactory receptor genes on chromosome 6 were significant after Bonferroni correction (α = 0.05/243345 = 2.05 × 10−7) with a high degree of linkage disequilibrium on 6p22.1 (p = 6.71 × 10−9). The differentially expressed gene analysis of autistic patients compared to controls in whole RNA sequencing identified significantly upregulated (foldchange ≥0.8 and p-value ≤ 0.05; n = 125) and downregulated (foldchange ≤−0.8 and p-value ≤ 0.05; n = 117) genes. The integration of significantly up- and downregulated genes and genes of significant SNPs identified regulatory variants (rs6657480, rs3130780, and rs1940475) associated with the up- (ITGB3BP) and downregulation (DDR1 and MMP8) of genes in autism spectrum disorder in people of Arab ancestries. The significant variants could be a biomarker of interest for identifying early autism among Arabs and helping to characterize the genes involved in the susceptibility mechanisms for autistic subjects. Full article
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Review

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24 pages, 446 KiB  
Review
Will the Use of Pharmacogenetics Improve Treatment Efficiency in COVID-19?
by Beata Franczyk, Jacek Rysz, Jarosław Miłoński, Tomasz Konecki, Magdalena Rysz-Górzyńska and Anna Gluba-Brzózka
Pharmaceuticals 2022, 15(6), 739; https://0-doi-org.brum.beds.ac.uk/10.3390/ph15060739 - 13 Jun 2022
Cited by 6 | Viewed by 2161
Abstract
The COVID-19 pandemic is associated with a global health crisis and the greatest challenge for scientists and doctors. The virus causes severe acute respiratory syndrome with an outcome that is fatal in more vulnerable populations. Due to the need to find an efficient [...] Read more.
The COVID-19 pandemic is associated with a global health crisis and the greatest challenge for scientists and doctors. The virus causes severe acute respiratory syndrome with an outcome that is fatal in more vulnerable populations. Due to the need to find an efficient treatment in a short time, there were several drugs that were repurposed or repositioned for COVID-19. There are many types of available COVID-19 therapies, including antiviral agents (remdesivir, lopinavir/ritonavir, oseltamivir), antibiotics (azithromycin), antiparasitics (chloroquine, hydroxychloroquine, ivermectin), and corticosteroids (dexamethasone). A combination of antivirals with various mechanisms of action may be more efficient. However, the use of some of these medicines can be related to the occurrence of adverse effects. Some promising drug candidates have been found to be ineffective in clinical trials. The knowledge of pharmacogenetic issues, which translate into variability in drug conversion from prodrug into drug, metabolism as well as transport, could help to predict treatment efficiency and the occurrence of adverse effects in patients. However, many drugs used for the treatment of COVID-19 have not undergone pharmacogenetic studies, perhaps as a result of the lack of time. Full article
34 pages, 3256 KiB  
Review
A Comprehensive Review of HLA and Severe Cutaneous Adverse Drug Reactions: Implication for Clinical Pharmacogenomics and Precision Medicine
by Chiraphat Kloypan, Napatrupron Koomdee, Patompong Satapornpong, Therdpong Tempark, Mohitosh Biswas and Chonlaphat Sukasem
Pharmaceuticals 2021, 14(11), 1077; https://0-doi-org.brum.beds.ac.uk/10.3390/ph14111077 - 25 Oct 2021
Cited by 27 | Viewed by 7042
Abstract
Human leukocyte antigen (HLA) encoded by the HLA gene is an important modulator for immune responses and drug hypersensitivity reactions as well. Genetic polymorphisms of HLA vary widely at population level and are responsible for developing severe cutaneous adverse drug reactions [...] Read more.
Human leukocyte antigen (HLA) encoded by the HLA gene is an important modulator for immune responses and drug hypersensitivity reactions as well. Genetic polymorphisms of HLA vary widely at population level and are responsible for developing severe cutaneous adverse drug reactions (SCARs) such as Stevens–Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), drug reaction with eosinophilia and systemic symptoms (DRESS), maculopapular exanthema (MPE). The associations of different HLA alleles with the risk of drug induced SJS/TEN, DRESS and MPE are strongly supportive for clinical considerations. Prescribing guidelines generated by different national and international working groups for translation of HLA pharmacogenetics into clinical practice are underway and functional in many countries, including Thailand. Cutting edge genomic technologies may accelerate wider adoption of HLA screening in routine clinical settings. There are great opportunities and several challenges as well for effective implementation of HLA genotyping globally in routine clinical practice for the prevention of drug induced SCARs substantially, enforcing precision medicine initiatives. Full article
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15 pages, 2853 KiB  
Review
Angiotensin-Converting Enzyme 2 (ACE2) in the Context of Respiratory Diseases and Its Importance in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection
by Enrique Ambrocio-Ortiz, Gloria Pérez-Rubio, Alma D. Del Ángel-Pablo, Ivette Buendía-Roldán, Leslie Chávez-Galán, Rafael de Jesús Hernández-Zenteno, Alejandra Ramírez-Venegas, Jorge Rojas-Serrano, Mayra Mejía, Rogelio Pérez-Padilla, Cristóbal Guadarrama-Pérez and Ramcés Falfán-Valencia
Pharmaceuticals 2021, 14(8), 805; https://0-doi-org.brum.beds.ac.uk/10.3390/ph14080805 - 17 Aug 2021
Cited by 7 | Viewed by 4051
Abstract
Angiotensin-Converting Enzyme 2 (ACE2) is an 805 amino acid protein encoded by the ACE2 gene expressed in various human cells, especially in those located in the epithelia. The primary function of ACE2 is to produce angiotensin (1–7) from angiotensin II (Ang II). The [...] Read more.
Angiotensin-Converting Enzyme 2 (ACE2) is an 805 amino acid protein encoded by the ACE2 gene expressed in various human cells, especially in those located in the epithelia. The primary function of ACE2 is to produce angiotensin (1–7) from angiotensin II (Ang II). The current research has described the importance of ACE2 and Ang (1–7) in alternative routes of the renin-angiotensin system (RAS) that promote the downregulation of fibrosis, inflammation, and oxidative stress processes in a great variety of diseases, such as hypertension, acute lung injury, liver cirrhosis, and kidney abnormalities. Investigations into the recent outbreak of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have revealed the importance of ACE2 during infection and its role in recognizing viral binding proteins through interactions with specific amino acids of this enzyme. Additionally, the ACE2 expression in several organs has allowed us to understand the clinical picture related to the infection caused by SARS-CoV-2. This review aims to provide context for the functions and importance of ACE2 with regards to SARS-CoV-2 in the general clinical aspect and its impact on other diseases, especially respiratory diseases. Full article
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39 pages, 377 KiB  
Review
Genomic Markers for Essential Tremor
by Félix Javier Jiménez-Jiménez, Hortensia Alonso-Navarro, Elena García-Martín, Ignacio Álvarez, Pau Pastor and José A. G. Agúndez
Pharmaceuticals 2021, 14(6), 516; https://0-doi-org.brum.beds.ac.uk/10.3390/ph14060516 - 27 May 2021
Cited by 15 | Viewed by 3816
Abstract
There are many reports suggesting an important role of genetic factors in the etiopathogenesis of essential tremor (ET), encouraging continuing the research for possible genetic markers. Linkage studies in families with ET have identified 4 genes/loci for familial ET, although the responsible gene(s) [...] Read more.
There are many reports suggesting an important role of genetic factors in the etiopathogenesis of essential tremor (ET), encouraging continuing the research for possible genetic markers. Linkage studies in families with ET have identified 4 genes/loci for familial ET, although the responsible gene(s) have not been identified. Genome-wide association studies (GWAS) described several variants in LINGO1, SLC1A2, STK32B, PPARGC1A, and CTNNA3, related with ET, but none of them have been confirmed in replication studies. In addition, the case-control association studies performed for candidate variants have not convincingly linked any gene with the risk for ET. Exome studies described the association of several genes with familial ET (FUS, HTRA2, TENM4, SORT1, SCN11A, NOTCH2NLC, NOS3, KCNS2, HAPLN4, USP46, CACNA1G, SLIT3, CCDC183, MMP10, and GPR151), but they were found only in singular families and, again, not found in other families or other populations, suggesting that some can be private polymorphisms. The search for responsible genes for ET is still ongoing. Full article
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