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Ibrahim R, Bahilo Martinez M, Dobson AJ. Rapamycin's lifespan effect is modulated by mito-nuclear epistasis in Drosophila. Aging Cell 2024:e14328. [PMID: 39225061 DOI: 10.1111/acel.14328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
The macrolide drug rapamycin is a benchmark anti-ageing drug, which robustly extends lifespan of diverse organisms. For any health intervention, it is paramount to establish whether benefits are distributed equitably among individuals and populations, and ideally to match intervention to recipients' needs. However, how responses to rapamycin vary is surprisingly understudied. Here we investigate how among-population variation in both mitochondrial and nuclear genetics shapes rapamycin's effects on lifespan. We show that epistatic "mito-nuclear" interactions, between mitochondria and nuclei, modulate the response to rapamycin treatment. Differences manifest as differential demographic effects of rapamycin, with altered age-specific mortality rate. However, a fitness cost of rapamycin early in life does not show a correlated response, suggesting that mito-nuclear epistasis can decouple costs and benefits of treatment. These findings suggest that a deeper understanding of how variation in mitochondrial and nuclear genomes shapes physiology may facilitate tailoring of anti-ageing therapy to individual need.
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Affiliation(s)
- Rita Ibrahim
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | | | - Adam J Dobson
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
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2
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Tečić Vuger A, Separovic R, Tolaney SM, Trapani D. Globalization of clinical research in oncology: Status, challenges, and future directions. J Cancer Policy 2024; 42:100500. [PMID: 39134147 DOI: 10.1016/j.jcpo.2024.100500] [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: 05/26/2024] [Accepted: 08/05/2024] [Indexed: 08/29/2024]
Abstract
PURPOSE Cancer is the second-leading cause of death worldwide, and its burden is increasing around the world, particularly in low- and middle-income countries (LMICs). Yet, cancer research has historically been conducted primarily in high-income countries (HICs). METHODS In this review, we describe the results of our literature search into the current state of international cancer trials, including the benefits, challenges, limitations, and ethical concerns regarding the international conduct of HIC-led trials. We also propose some possible means of addressing these challenges and overcoming these barriers to extend the benefits of cancer research to people around the world. RESULTS Over the last several decades, there has been a shift toward inclusion of investigators and participants from LMICs in pivotal cancer clinical trials. CONCLUSIONS While inclusion of LMIC countries has benefits, including increased diversity of participant populations, investment in research infrastructure in LMICs, and potential expansion of cancer treatment options around the world, the continued leadership of most trials by HICs presents ethical concerns, including potential exploitation of researchers and participants from LMICs, lack of focus on cancer types prevalent in all participating regions, and disparities in access to approved therapies once the trial is complete.
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Affiliation(s)
- Ana Tečić Vuger
- University Hospital for Tumors, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Robert Separovic
- University Hospital for Tumors, Sestre milosrdnice University Hospital Center, Zagreb, Croatia; University of Josip Juraj Strossmayer, Osijek, Croatia; University of Juraj Dobrila, Pula, Croatia
| | | | - Dario Trapani
- European Institute of Oncology, IRCCS, Milan, Italy; University of Milan, Department of Oncology and Hematology, Milan, Italy; Department of Pharmaceutical Sciences, Università del Piemonte Orientale (UNIUPO) "Amedeo Avogadro", Novara, Italy.
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3
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Mann V, Sundaresan A, Shishodia S. Overnutrition and Lipotoxicity: Impaired Efferocytosis and Chronic Inflammation as Precursors to Multifaceted Disease Pathogenesis. BIOLOGY 2024; 13:241. [PMID: 38666853 PMCID: PMC11048223 DOI: 10.3390/biology13040241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Overnutrition, driven by the consumption of high-fat, high-sugar diets, has reached epidemic proportions and poses a significant global health challenge. Prolonged overnutrition leads to the deposition of excessive lipids in adipose and non-adipose tissues, a condition known as lipotoxicity. The intricate interplay between overnutrition-induced lipotoxicity and the immune system plays a pivotal role in the pathogenesis of various diseases. This review aims to elucidate the consequences of impaired efferocytosis, caused by lipotoxicity-poisoned macrophages, leading to chronic inflammation and the subsequent development of severe infectious diseases, autoimmunity, and cancer, as well as chronic pulmonary and cardiovascular diseases. Chronic overnutrition promotes adipose tissue expansion which induces cellular stress and inflammatory responses, contributing to insulin resistance, dyslipidemia, and metabolic syndrome. Moreover, sustained exposure to lipotoxicity impairs the efferocytic capacity of macrophages, compromising their ability to efficiently engulf and remove dead cells. The unresolved chronic inflammation perpetuates a pro-inflammatory microenvironment, exacerbating tissue damage and promoting the development of various diseases. The interaction between overnutrition, lipotoxicity, and impaired efferocytosis highlights a critical pathway through which chronic inflammation emerges, facilitating the development of severe infectious diseases, autoimmunity, cancer, and chronic pulmonary and cardiovascular diseases. Understanding these intricate connections sheds light on potential therapeutic avenues to mitigate the detrimental effects of overnutrition and lipotoxicity on immune function and tissue homeostasis, thereby paving the way for novel interventions aimed at reducing the burden of these multifaceted diseases on global health.
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Affiliation(s)
| | | | - Shishir Shishodia
- Department of Biology, Texas Southern University, Houston, TX 77004, USA; (V.M.); (A.S.)
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4
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Paliwal A, Jain S, Kumar S, Wal P, Khandai M, Khandige PS, Sadananda V, Anwer MK, Gulati M, Behl T, Srivastava S. Predictive Modelling in pharmacokinetics: from in-silico simulations to personalized medicine. Expert Opin Drug Metab Toxicol 2024; 20:181-195. [PMID: 38480460 DOI: 10.1080/17425255.2024.2330666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Pharmacokinetic parameters assessment is a critical aspect of drug discovery and development, yet challenges persist due to limited training data. Despite advancements in machine learning and in-silico predictions, scarcity of data hampers accurate prediction of drug candidates' pharmacokinetic properties. AREAS COVERED The study highlights current developments in human pharmacokinetic prediction, talks about attempts to apply synthetic approaches for molecular design, and searches several databases, including Scopus, PubMed, Web of Science, and Google Scholar. The article stresses importance of rigorous analysis of machine learning model performance in assessing progress and explores molecular modeling (MM) techniques, descriptors, and mathematical approaches. Transitioning to clinical drug development, article highlights AI (Artificial Intelligence) based computer models optimizing trial design, patient selection, dosing strategies, and biomarker identification. In-silico models, including molecular interactomes and virtual patients, predict drug performance across diverse profiles, underlining the need to align model results with clinical studies for reliability. Specialized training for human specialists in navigating predictive models is deemed critical. Pharmacogenomics, integral to personalized medicine, utilizes predictive modeling to anticipate patient responses, contributing to more efficient healthcare system. Challenges in realizing potential of predictive modeling, including ethical considerations and data privacy concerns, are acknowledged. EXPERT OPINION AI models are crucial in drug development, optimizing trials, patient selection, dosing, and biomarker identification and hold promise for streamlining clinical investigations.
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Affiliation(s)
- Ajita Paliwal
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, India
| | - Smita Jain
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, India
| | - Sachin Kumar
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, India
| | - Pranay Wal
- Department of Pharmacy, Pranveer Singh Institute of Technology, Pharmacy, Kanpur, India
| | - Madhusmruti Khandai
- Department of Pharmacy, Royal College of Pharmacy and Health Sciences, Berahmpur, India
| | - Prasanna Shama Khandige
- NGSM Institute of Pharmaceutical Sciences, Department of Pharmacology, Manglauru, NITTE (Deemed to be University), Manglauru, India
| | - Vandana Sadananda
- AB Shetty Memorial Institute of Dental Sciences, Department of Conservative Dentistry and Endodontics, NITTE (Deemed to be University), Mangaluru, India
| | - Md Khalid Anwer
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
- ARCCIM, Health, University of Technology, Sydney, Ultimo, Australia
| | - Tapan Behl
- Amity School of Pharmaceutical Sciences, Amity University, Mohali, Punjab, India
| | - Shriyansh Srivastava
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, India
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, India
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5
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Raupach L, Königs C. PharmoCo: a graph-based visualization of pharmacogenomic plausibility check reports for clinical decision support systems. J Integr Bioinform 2023; 20:jib-2023-0026. [PMID: 38150373 PMCID: PMC10777363 DOI: 10.1515/jib-2023-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/08/2023] [Indexed: 12/29/2023] Open
Abstract
The first approaches in recent years for the integration of pharmacogenomic plausibility checks into clinical practice show both a promising improvement in the drug therapy safety, but also difficulties in application. One of the difficulties is the meaningful interpretation of the text-based results by the medical practitioner. We propose here as an appropriate and sensible solution to avoid misunderstandings and to include evidence-based, pharmacogenomic recommendations in prescriptions, which should be the graph-based visualization of the reports. This allows for a plausible interpretation and relate complex, even contradictory guidelines. The improved overview over the pharmacogenomics (PGx) guidelines using the graphical visualization makes the medical practitioner's choice of dose and medication more patient-specific, improves the treatment outcome and thus, increases the drug therapy safety.
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Affiliation(s)
- Lena Raupach
- Faculty of Technology, Bioinformatics/Medical Informatics Department, Bielefeld University, D-33501Bielefeld, Germany
- ID Information und Dokumentation im Gesundheitswesen GmbH & Co. KGaA, D-10115Berlin, Germany
| | - Cassandra Königs
- Faculty of Technology, Bioinformatics/Medical Informatics Department, Bielefeld University, D-33501Bielefeld, Germany
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6
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Guin D, Hasija Y, Kukreti R. Assessment of clinically actionable pharmacogenetic markers to stratify anti-seizure medications. THE PHARMACOGENOMICS JOURNAL 2023; 23:149-160. [PMID: 37626111 DOI: 10.1038/s41397-023-00313-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 07/22/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
Abstract
Epilepsy treatment is challenging due to heterogeneous syndromes, different seizure types and higher inter-individual variability. Identification of genetic variants predicting drug efficacy, tolerability and risk of adverse-effects for anti-seizure medications (ASMs) is essential. Here, we assessed the clinical actionability of known genetic variants, based on their functional and clinical significance and estimated their diagnostic predictability. We performed a systematic PubMed search to identify articles with pharmacogenomic (PGx) information for forty known ASMs. Functional annotation of the identified genetic variants was performed using different in silico tools, and their clinical significance was assessed using the American College of Medical Genetics (ACMG) guidelines for variant pathogenicity, level of evidence (LOE) from PharmGKB and the United States-Food and drug administration (US- FDA) drug labelling with PGx information. Diagnostic predictability of the replicated genetic variants was evaluated by calculating their accuracy. A total of 270 articles were retrieved with PGx evidence associated with 19 ASMs including 178 variants across 93 genes, classifying 26 genetic variants as benign/ likely benign, fourteen as drug response markers and three as risk factors for drug response. Only seventeen of these were replicated, with accuracy (up to 95%) in predicting PGx outcomes specific to six ASMs. Eight out of seventeen variants have FDA-approved PGx drug labelling for clinical implementation. Therefore, the remaining nine variants promise for potential clinical actionability and can be improvised with additional experimental evidence for clinical utility.
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Affiliation(s)
- Debleena Guin
- Genomics and Molecular Medicine Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, 110007, India
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Delhi, 110042, India
| | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Delhi, 110042, India
| | - Ritushree Kukreti
- Genomics and Molecular Medicine Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, 110007, India.
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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7
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Mansueto G, Lanza G, Falleti J, Orabona P, Alaouieh D, Hong E, Girolami S, Montella M, Fisicaro F, Galdieri A, Singh P, Di Napoli M. Central and Peripheral Nervous System Complications of Vasculitis Syndromes from Pathology to Bedside: Part 2-Peripheral Nervous System. Curr Neurol Neurosci Rep 2023; 23:83-107. [PMID: 36820992 PMCID: PMC9947450 DOI: 10.1007/s11910-023-01249-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2023] [Indexed: 02/24/2023]
Abstract
PURPOSE OF REVIEW Peripheral nervous system vasculitides (PNSV) are a heterogeneous group of disorders with a clinical subset that may differ in prognosis and therapy. We provide a comprehensive update on the clinical assessment, diagnosis, complications, treatment, and follow-up of PNSV. RECENT FINDINGS Progress in neuroimaging, molecular testing, and peripheral nerve biopsy has improved clinical assessment and decision-making of PNSV, also providing novel insights on how to prevent misdiagnosis and increase diagnostic certainty. Advances in imaging techniques, allowing to clearly display the vessel walls, have also enhanced the possibility to differentiate inflammatory from non-inflammatory vascular lesions, while recent histopathology data have identified the main morphological criteria for more accurate diagnosis and differential diagnoses. Overall, the identification of peculiar morphological findings tends to improve diagnostic accuracy by defining a clearer boundary between systemic and non-systemic neuropathies. Therefore, the definition of epineurium vessel wall damage, type of vascular lesion, characterization of lymphocyte populations, antibodies, and inflammatory factors, as well as the identification of direct nerve damage or degeneration, are the common goals for pathologists and clinicians, who will both benefit for data integration and findings translation. Nevertheless, to date, treatment is still largely empiric and, in some cases, unsatisfactory, thus often precluding precise prognostic prediction. In this context, new diagnostic techniques and multidisciplinary management will be essential in the proper diagnosis and prompt management of PNSV, as highlighted in the present review. Thirty to fifty percent of all patients with vasculitis have signs of polyneuropathy. Neuropathies associated with systemic vasculitis are best managed according to the guidelines of the underlying disease because appropriate workup and initiation of treatment can reduce morbidity. Steroids, or in severe or progressive cases, cyclophosphamide pulse therapy is the standard therapy in non-systemic vasculitic neuropathies. Some patients need long-term immunosuppression. The use of novel technologies for high-throughput genotyping will permit to determine the genetic influence of related phenotypes in patients with PNSV.
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Affiliation(s)
- Gelsomina Mansueto
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Piazza L. Miraglia 2, 80138, Naples, Italy.,Clinical Department of Laboratory Services and Public Health-Legal Medicine Unit, University of Campania "Luigi Vanvitelli", Via Luciano Armanni 5, 80138, Naples, Italy.,Pathology-Unit of Federico II University, Via S. Pansini 3, 80131, Naples, Italy
| | - Giuseppe Lanza
- Department of Surgery and Medical-Surgical Specialties, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy.,Clinical Neurophysiology Research Unit, Oasi Research Institute-IRCCS, Via Conte Ruggero 73, 94018, Troina, Italy
| | - Jessica Falleti
- Pathology Unit, Sant'Anna E San Sebastiano Hospital, 81100, Caserta, Italy
| | - Pasquale Orabona
- Pathology Unit, Sant'Anna E San Sebastiano Hospital, 81100, Caserta, Italy
| | | | - Emily Hong
- School of Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Sara Girolami
- Neurological Service, SS Annunziata Hospital, Viale Mazzini 100, 67039, Sulmona, L'Aquila, Italy
| | - Marco Montella
- Mental and Physical Health and Preventive Medicine Department, University of Campania "Luigi Vanvitelli", Via Luciano Armanni 5, 80138, Naples, Italy
| | - Francesco Fisicaro
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia 97, 95123, Catania, Italy
| | - Anna Galdieri
- AOU "Luigi Vanvitelli", Via Santa Maria Di Costantinopoli 104, 80138, Naples, Italy
| | - Puneetpal Singh
- Department of Human Genetics, Punjabi University, Patiala, 147002, Punjab, India
| | - Mario Di Napoli
- Neurological Service, SS Annunziata Hospital, Viale Mazzini 100, 67039, Sulmona, L'Aquila, Italy.
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8
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Mallah N, Zapata-Cachafeiro M, Aguirre C, Ibarra-García E, Palacios-Zabalza I, Macías-García F, Piñeiro-Lamas M, Ibáñez L, Vidal X, Vendrell L, Martin-Arias L, Sáinz-Gil M, Velasco-González V, Bacariza-Cortiñas M, Salgado A, Estany-Gestal A, Figueiras A. Synergism interaction between genetic polymorphisms in drug metabolizing enzymes and NSAIDs on upper gastrointestinal haemorrhage: a multicenter case-control study. Ann Med 2022; 54:379-392. [PMID: 35114859 PMCID: PMC8820810 DOI: 10.1080/07853890.2021.2016940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Interindividual genetic variations contribute to differences in patients' response to drugs as well as to the development of certain disorders. Patients who use non-steroidal anti-inflammatory drugs (NSAIDs) may develop serious gastrointestinal disorders, mainly upper gastrointestinal haemorrhage (UGIH). Studies about the interaction between NSAIDs and genetic variations on the risk of UGIH are scarce. Therefore, we investigated the effect of 16 single nucleotide polymorphisms (SNPs) involved in drug metabolism on the risk of NSAIDs-induced UGIH. MATERIALS AND METHODS We conducted a multicenter case-control study of 326 cases and 748 controls. Participants were sub-grouped into four categories according to NSAID exposure and genetic profile. We estimated odds ratios (ORs) and their 95% confidence intervals (CI) using generalized linear mixed models for dependent binomial variables and then calculated the measures of interaction, synergism index (S), and relative excess risk due to interaction (RERI). We undertook stratified analyses by the type of NSAID (aspirin, non-aspirin). RESULTS We observed an excess risk of UGIH due to an interaction between any NSAID, non-aspirin NSAIDs or aspirin and carrying certain SNPs. The greatest excess risk was observed for carriers of: rs2180314:C>G [any NSAID: S = 3.30 (95%CI: 1.24-8.80), RERI = 4.39 (95%CI: 0.70-8.07); non-aspirin NSAIDs: S = 3.42 (95%CI: 1.12-10.47), RERI = 3.97 (95%CI: 0.44-7.50)], and rs4809957:A>G [any NSAID: S = 2.11 (95%CI: 0.90-4.97), RERI = 3.46 (95%CI: -0.40-7.31)]. Aspirin use by carriers of rs6664:C>T is also associated with increased risk of UGIH [ORaspirin(+),wild-type: 2.22 (95%CI: 0.69-7.17) vs. ORaspirin(+),genetic-variation: 7.72 (95%CI: 2.75-21.68)], yet larger sample size is needed to confirm this observation. CONCLUSIONS The joint effect of the SNPs s2180314:C>G and rs4809957:A>G and NSAIDs are more than three times higher than the sum of their individual effects. Personalized prescriptions based on genotyping would permit a better weighing of risks and benefits from NSAID consumption.KEY MESSAGESMulticenter case-control study of the effect of genetic variations involved in drug metabolism on upper gastrointestinal haemorrhage (UGIH) induced by NSAIDs (aspirin and non-aspirin).There is a statistically significant additive synergism interaction between certain genetic polymorphisms and NSAIDs on UGIH: rs2180314:C>G and rs4809957:A>G. The joint effect of each of these single nucleotide polymorphisms and NSAIDs on UGIH is more than three times higher than the sum of their individual effects.Genetic profiling and personalized prescriptions would be useful in managing the risks and benefits associated with NSAIDs.
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Affiliation(s)
- Narmeen Mallah
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain.,WHO Collaborating Centre for Vaccine Safety, Santiago de Compostela, Spain.,Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Carlos III Health Institute, Madrid, Spain
| | - Maruxa Zapata-Cachafeiro
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain.,Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública-CIBERESP), Carlos III Health Institute, Madrid, Spain
| | - Carmelo Aguirre
- Pharmacotherapy Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Basque Country Pharmacovigilance Unit, University Hospital of Galdakao-Usansolo, Osakidetza, Spain.,Pharmacology Department, Medicine and Nursing Faculty, University of the Basque Country, Barakaldo, Spain
| | - Eguzkiñe Ibarra-García
- Pharmacotherapy Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Osakidetza Basque Health Service, Pharmacy Department, Urduliz Hospital, Urduliz, Spain
| | - Itziar Palacios-Zabalza
- Pharmacotherapy Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Basque Country Pharmacovigilance Unit, University Hospital of Galdakao-Usansolo, Osakidetza, Spain
| | - Fernando Macías-García
- Department of Gastroenterology and Hepatology, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - María Piñeiro-Lamas
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública-CIBERESP), Carlos III Health Institute, Madrid, Spain.,Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Luisa Ibáñez
- Department of Pharmacology, Therapeutics and Toxicology, Catalonian Institute of Pharmacology, Clinical Pharmacology Service, Vall d'Hebron University Teaching Hospital, Autonomous University, Barcelona, Spain
| | - Xavier Vidal
- Department of Pharmacology, Therapeutics and Toxicology, Catalonian Institute of Pharmacology, Clinical Pharmacology Service, Vall d'Hebron University Teaching Hospital, Autonomous University, Barcelona, Spain
| | - Lourdes Vendrell
- Department of Pharmacology, Therapeutics and Toxicology, Catalonian Institute of Pharmacology, Clinical Pharmacology Service, Vall d'Hebron University Teaching Hospital, Autonomous University, Barcelona, Spain
| | - Luis Martin-Arias
- Centre for Research on Drug Safety (CESME), Valladolid University, Valladolid, Spain
| | - María Sáinz-Gil
- Centre for Research on Drug Safety (CESME), Valladolid University, Valladolid, Spain
| | | | | | - Angel Salgado
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Estany-Gestal
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Adolfo Figueiras
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain.,Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública-CIBERESP), Carlos III Health Institute, Madrid, Spain.,Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
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9
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Luke MJ, Krupetsky N, Liu H, Korenvain C, Crown N, Toenjes S, Sproule BA, Piquette-Miller M, Guirguis LM, McCarthy LM. Pharmacists as Personalized Medicine Experts (PRIME): Experiences Implementing Pharmacist-Led Pharmacogenomic Testing in Primary Care Practices. PHARMACY 2021; 9:pharmacy9040201. [PMID: 34941633 PMCID: PMC8709167 DOI: 10.3390/pharmacy9040201] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 12/01/2022] Open
Abstract
Research exploring the integration of pharmacogenomics (PGx) testing by pharmacists into their primary care practices (including community pharmacies) has focused on the “external” factors that impact practice implementation. In this study, additional “internal” factors, related to the capabilities, opportunities, and motivations of pharmacists that influence their ability to implement PGx testing, were analyzed. Semi-structured interview data from the Pharmacists as Personalized Medicine Experts (PRIME) study, which examined the barriers and facilitators to implementing PGx testing by pharmacists into primary care practice, were analyzed. Through thematic analysis, using the theoretical domains framework (TDF) domains as deductive codes, the authors identified the most relevant TDF domains and applied the behavioural change wheel (BCW) to generate intervention types to aid in the implementation of PGx testing. Pharmacists described how their professional identities, practice environments, self-confidence, and beliefs in the benefits of PGx impacted their ability to provide a PGx-testing service. Potential interventions to improve the implementation of the PGx service included preparing pharmacists for managing an increased patient load, helping pharmacists navigate the software and technology requirements associated with the PGx service, and streamlining workflows and documentation requirements. As interest in the wide-scale implementation of PGx testing through community pharmacies grows, additional strategies need to address the “internal” factors that influence the ability of pharmacists to integrate testing into their practices.
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Affiliation(s)
- Miles J. Luke
- Pharmacy Services, Women’s College Hospital, Toronto, ON M5S 1B2, Canada; (M.J.L.); (N.K.); (C.K.); (N.C.); (S.T.)
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; (H.L.); (B.A.S.); (M.P.-M.)
| | - Nina Krupetsky
- Pharmacy Services, Women’s College Hospital, Toronto, ON M5S 1B2, Canada; (M.J.L.); (N.K.); (C.K.); (N.C.); (S.T.)
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; (H.L.); (B.A.S.); (M.P.-M.)
| | - Helen Liu
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; (H.L.); (B.A.S.); (M.P.-M.)
| | - Clara Korenvain
- Pharmacy Services, Women’s College Hospital, Toronto, ON M5S 1B2, Canada; (M.J.L.); (N.K.); (C.K.); (N.C.); (S.T.)
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; (H.L.); (B.A.S.); (M.P.-M.)
| | - Natalie Crown
- Pharmacy Services, Women’s College Hospital, Toronto, ON M5S 1B2, Canada; (M.J.L.); (N.K.); (C.K.); (N.C.); (S.T.)
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; (H.L.); (B.A.S.); (M.P.-M.)
| | - Sameera Toenjes
- Pharmacy Services, Women’s College Hospital, Toronto, ON M5S 1B2, Canada; (M.J.L.); (N.K.); (C.K.); (N.C.); (S.T.)
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; (H.L.); (B.A.S.); (M.P.-M.)
| | - Beth A. Sproule
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; (H.L.); (B.A.S.); (M.P.-M.)
- Center for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Micheline Piquette-Miller
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; (H.L.); (B.A.S.); (M.P.-M.)
| | - Lisa M. Guirguis
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 1C9, Canada;
| | - Lisa M. McCarthy
- Pharmacy Services, Women’s College Hospital, Toronto, ON M5S 1B2, Canada; (M.J.L.); (N.K.); (C.K.); (N.C.); (S.T.)
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; (H.L.); (B.A.S.); (M.P.-M.)
- Institute for Better Health, Trillium Health Partners, Mississauga, ON L5B 1B8, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada
- Women’s College Research Institute, Women’s College Hospital, Toronto, ON M5S 1B2, Canada
- Correspondence:
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10
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Jayakar S, Shim J, Jo S, Bean BP, Singeç I, Woolf CJ. Developing nociceptor-selective treatments for acute and chronic pain. Sci Transl Med 2021; 13:eabj9837. [PMID: 34757806 PMCID: PMC9964063 DOI: 10.1126/scitranslmed.abj9837] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite substantial efforts dedicated to the development of new, nonaddictive analgesics, success in treating pain has been limited. Clinically available analgesic agents generally lack efficacy and may have undesirable side effects. Traditional target-based drug discovery efforts that generate compounds with selectivity for single targets have a high rate of attrition because of their poor clinical efficacy. Here, we examine the challenges associated with the current analgesic drug discovery model and review evidence in favor of stem cell–derived neuronal-based screening approaches for the identification of analgesic targets and compounds for treating diverse forms of acute and chronic pain.
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Affiliation(s)
- Selwyn Jayakar
- F.M. Kirby Neurobiology, Boston Children’s Hospital, and Department of Neurology, Harvard Medical School; Boston, MA 02115, USA
| | - Jaehoon Shim
- F.M. Kirby Neurobiology, Boston Children’s Hospital, and Department of Neurology, Harvard Medical School; Boston, MA 02115, USA
| | - Sooyeon Jo
- Department of Neurobiology, Harvard Medical School; Boston, MA 02115, USA
| | - Bruce P Bean
- Department of Neurobiology, Harvard Medical School; Boston, MA 02115, USA
| | - Ilyas Singeç
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH); Bethesda, MD 20892, USA
| | - Clifford J Woolf
- F.M. Kirby Neurobiology, Boston Children’s Hospital, and Department of Neurology, Harvard Medical School; Boston, MA 02115, USA
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11
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Tafazoli A, Guchelaar HJ, Miltyk W, Kretowski AJ, Swen JJ. Applying Next-Generation Sequencing Platforms for Pharmacogenomic Testing in Clinical Practice. Front Pharmacol 2021; 12:693453. [PMID: 34512329 PMCID: PMC8424415 DOI: 10.3389/fphar.2021.693453] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Pharmacogenomics (PGx) studies the use of genetic data to optimize drug therapy. Numerous clinical centers have commenced implementing pharmacogenetic tests in clinical routines. Next-generation sequencing (NGS) technologies are emerging as a more comprehensive and time- and cost-effective approach in PGx. This review presents the main considerations for applying NGS in guiding drug treatment in clinical practice. It discusses both the advantages and the challenges of implementing NGS-based tests in PGx. Moreover, the limitations of each NGS platform are revealed, and the solutions for setting up and management of these technologies in clinical practice are addressed.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, Bialystok, Poland
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Network of Personalized Therapeutics, Leiden, Netherlands
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Adam J. Kretowski
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Jesse J. Swen
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Network of Personalized Therapeutics, Leiden, Netherlands
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12
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Yehya A, Matalgah L. Toward Interprofessional Education of Pharmacogenomics: An Interdisciplinary Assessment. Pharmacology 2021; 106:534-541. [PMID: 34304231 DOI: 10.1159/000517385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 05/18/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Pharmacogenomics, which emerged from disciplines such as pharmacology and genetics, is an increasingly important interdisciplinary field of health research, as indicated by the rapid growth of related literature. The aim of this study was to evaluate knowledge among genetics and pharmacology health-care students and to evaluate their exposure to and perceptions of pharmacogenomics. METHODS An anonymous, 28-item online survey was distributed to medical and pharmacy students enrolled at Yarmouk University, Jordan. RESULTS The respondents (n = 300) had an overall moderate level of knowledge regarding genetics and pharmacology. Most respondents recognized the benefits of pharmacogenomics for therapy optimization, but they had insufficient exposure to the topic. Most respondents supported providing pharmacogenetic testing in Jordan. The most preferred educational format in pharmacogenomics was integration in pharmacology courses. DISCUSSION/CONCLUSION Medical and pharmacy students are becoming increasingly aware of the importance of pharmacogenomics in therapy optimization. Challenges such as the complexity of the topic and low retention of previous knowledge should be addressed to promote pharmacogenomics education. More work is needed to increase students' exposure to pharmacogenomics information. A deeper integration of pharmacogenomics applications into pharmacology courses is proposed to emphasize applications of pharmacogenomics.
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Affiliation(s)
- Alaa Yehya
- Department of Clinical Pharmacy and Pharmacy Practice, Irbid, Jordan
| | - Laila Matalgah
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan
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13
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Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA. The influence of evolutionary history on human health and disease. Nat Rev Genet 2021; 22:269-283. [PMID: 33408383 PMCID: PMC7787134 DOI: 10.1038/s41576-020-00305-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2020] [Indexed: 01/29/2023]
Abstract
Nearly all genetic variants that influence disease risk have human-specific origins; however, the systems they influence have ancient roots that often trace back to evolutionary events long before the origin of humans. Here, we review how advances in our understanding of the genetic architectures of diseases, recent human evolution and deep evolutionary history can help explain how and why humans in modern environments become ill. Human populations exhibit differences in the prevalence of many common and rare genetic diseases. These differences are largely the result of the diverse environmental, cultural, demographic and genetic histories of modern human populations. Synthesizing our growing knowledge of evolutionary history with genetic medicine, while accounting for environmental and social factors, will help to achieve the promise of personalized genomics and realize the potential hidden in an individual's DNA sequence to guide clinical decisions. In short, precision medicine is fundamentally evolutionary medicine, and integration of evolutionary perspectives into the clinic will support the realization of its full potential.
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Affiliation(s)
- Mary Lauren Benton
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.252890.40000 0001 2111 2894Department of Computer Science, Baylor University, Waco, TX USA
| | - Abin Abraham
- grid.152326.10000 0001 2264 7217Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN USA
| | - Abigail L. LaBella
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - Patrick Abbot
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - Antonis Rokas
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - John A. Capra
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA ,grid.266102.10000 0001 2297 6811Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA USA
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14
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Hassan R, Allali I, Agamah FE, Elsheikh SSM, Thomford NE, Dandara C, Chimusa ER. Drug response in association with pharmacogenomics and pharmacomicrobiomics: towards a better personalized medicine. Brief Bioinform 2020; 22:6012864. [PMID: 33253350 DOI: 10.1093/bib/bbaa292] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/19/2020] [Accepted: 10/03/2020] [Indexed: 12/15/2022] Open
Abstract
Researchers have long been presented with the challenge imposed by the role of genetic heterogeneity in drug response. For many years, Pharmacogenomics and pharmacomicrobiomics has been investigating the influence of an individual's genetic background to drug response and disposition. More recently, the human gut microbiome has proven to play a crucial role in the way patients respond to different therapeutic drugs and it has been shown that by understanding the composition of the human microbiome, we can improve the drug efficacy and effectively identify drug targets. However, our knowledge on the effect of host genetics on specific gut microbes related to variation in drug metabolizing enzymes, the drug remains limited and therefore limits the application of joint host-microbiome genome-wide association studies. In this paper, we provide a historical overview of the complex interactions between the host, human microbiome and drugs. While discussing applications, challenges and opportunities of these studies, we draw attention to the critical need for inclusion of diverse populations and the development of an innovative and combined pharmacogenomics and pharmacomicrobiomics approach, that may provide an important basis in personalized medicine.
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Affiliation(s)
- Radia Hassan
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | - Imane Allali
- Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Morocco
| | - Francis E Agamah
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | | | - Nicholas E Thomford
- Lecturers at the Department of Medical Biochemistry School of Medical Sciences, University of Cape Coast, Ghana
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town
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15
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Woodward KE, de Jesus P, Esser MJ. Neuroinflammation and Precision Medicine in Pediatric Neurocritical Care: Multi-Modal Monitoring of Immunometabolic Dysfunction. Int J Mol Sci 2020; 21:E9155. [PMID: 33271778 PMCID: PMC7730047 DOI: 10.3390/ijms21239155] [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: 10/22/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 11/17/2022] Open
Abstract
The understanding of molecular biology in neurocritical care (NCC) is expanding rapidly and recognizing the important contribution of neuroinflammation, specifically changes in immunometabolism, towards pathological disease processes encountered across all illnesses in the NCC. Additionally, the importance of individualized inflammatory responses has been emphasized, acknowledging that not all individuals have the same mechanisms contributing towards their presentation. By understanding cellular processes that drive disease, we can make better personalized therapy decisions to improve patient outcomes. While the understanding of these cellular processes is evolving, the ability to measure such cellular responses at bedside to make acute care decisions is lacking. In this overview, we review cellular mechanisms involved in pathological neuroinflammation with a focus on immunometabolic dysfunction and review non-invasive bedside tools that have the potential to measure indirect and direct markers of shifts in cellular metabolism related to neuroinflammation. These tools include near-infrared spectroscopy, transcranial doppler, elastography, electroencephalography, magnetic resonance imaging and spectroscopy, and cytokine analysis. Additionally, we review the importance of genetic testing in providing information about unique metabolic profiles to guide individualized interpretation of bedside data. Together in tandem, these modalities have the potential to provide real time information and guide more informed treatment decisions.
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Affiliation(s)
| | | | - Michael J. Esser
- Alberta Children’s Hospital, University of Calgary, Calgary, AB T3B 6A8, Canada; (K.E.W.); (P.d.J.)
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16
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Cocchi E, Nestor JG, Gharavi AG. Clinical Genetic Screening in Adult Patients with Kidney Disease. Clin J Am Soc Nephrol 2020; 15:1497-1510. [PMID: 32646915 PMCID: PMC7536756 DOI: 10.2215/cjn.15141219] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Expanded accessibility of genetic sequencing technologies, such as chromosomal microarray and massively parallel sequencing approaches, is changing the management of hereditary kidney diseases. Genetic causes account for a substantial proportion of pediatric kidney disease cases, and with increased utilization of diagnostic genetic testing in nephrology, they are now also detected at appreciable frequencies in adult populations. Establishing a molecular diagnosis can have many potential benefits for patient care, such as guiding treatment, familial testing, and providing deeper insights on the molecular pathogenesis of kidney diseases. Today, with wider clinical use of genetic testing as part of the diagnostic evaluation, nephrologists have the challenging task of selecting the most suitable genetic test for each patient, and then applying the results into the appropriate clinical contexts. This review is intended to familiarize nephrologists with the various technical, logistical, and ethical considerations accompanying the increasing utilization of genetic testing in nephrology care.
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Affiliation(s)
- Enrico Cocchi
- Division of Nephrology and Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, New York
- Department of Pediatrics, Universita' degli Studi di Torino, Torino, Italy
| | - Jordan Gabriela Nestor
- Division of Nephrology and Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, New York
| | - Ali G Gharavi
- Division of Nephrology and Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, New York
- Insititute of Genomic Medicine, Columbia University, New York, New York
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17
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Ovics P, Regev D, Baskin P, Davidor M, Shemer Y, Neeman S, Ben-Haim Y, Binah O. Drug Development and the Use of Induced Pluripotent Stem Cell-Derived Cardiomyocytes for Disease Modeling and Drug Toxicity Screening. Int J Mol Sci 2020; 21:E7320. [PMID: 33023024 PMCID: PMC7582587 DOI: 10.3390/ijms21197320] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/23/2020] [Accepted: 09/27/2020] [Indexed: 12/19/2022] Open
Abstract
: Over the years, numerous groups have employed human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) as a superb human-compatible model for investigating the function and dysfunction of cardiomyocytes, drug screening and toxicity, disease modeling and for the development of novel drugs for heart diseases. In this review, we discuss the broad use of iPSC-CMs for drug development and disease modeling, in two related themes. In the first theme-drug development, adverse drug reactions, mechanisms of cardiotoxicity and the need for efficient drug screening protocols-we discuss the critical need to screen old and new drugs, the process of drug development, marketing and Adverse Drug reactions (ADRs), drug-induced cardiotoxicity, safety screening during drug development, drug development and patient-specific effect and different mechanisms of ADRs. In the second theme-using iPSC-CMs for disease modeling and developing novel drugs for heart diseases-we discuss the rationale for using iPSC-CMs and modeling acquired and inherited heart diseases with iPSC-CMs.
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Affiliation(s)
- Paz Ovics
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Danielle Regev
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Polina Baskin
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Mor Davidor
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Yuval Shemer
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Shunit Neeman
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
| | - Yael Ben-Haim
- Institute of Molecular and Clinical Sciences, St. George’s University of London, London SW17 0RE, UK;
- Cardiology Clinical Academic Group, St. George’s University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Ofer Binah
- Department of Physiology, Biophysics and Systems Biology, The Rappaport Institute, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel; (P.O.); (D.R.); (P.B.); (M.D.); (Y.S.); (S.N.)
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18
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Makvandi P, Ghomi M, Ashrafizadeh M, Tafazoli A, Agarwal T, Delfi M, Akhtari J, Zare EN, Padil VVT, Zarrabi A, Pourreza N, Miltyk W, Maiti TK. A review on advances in graphene-derivative/polysaccharide bionanocomposites: Therapeutics, pharmacogenomics and toxicity. Carbohydr Polym 2020; 250:116952. [PMID: 33049857 DOI: 10.1016/j.carbpol.2020.116952] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/17/2022]
Abstract
Graphene-based bionanocomposites are employed in several ailments, such as cancers and infectious diseases, due to their large surface area (to carry drugs), photothermal properties, and ease of their functionalization (owing to their active groups). Modification of graphene-derivatives with polysaccharides is a promising strategy to decrease their toxicity and improve target ability, which consequently enhances their biotherapeutic efficacy. Herein, functionalization of graphene-based materials with carbohydrate polymers (e.g., chitosan, starch, alginate, hyaluronic acid, and cellulose) are presented. Subsequently, recent advances in graphene nanomaterial/polysaccharide-based bionanocomposites in infection treatment and cancer therapy are comprehensively discussed. Pharmacogenomic and toxicity assessments for these bionanocomposites are also highlighted to provide insight for future optimized and smart investigations and researches.
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Affiliation(s)
- Pooyan Makvandi
- Istituto Italiano di Tecnologia, Centre for Micro-BioRobotics, viale Rinaldo Piaggio 34, Pontedera, Pisa, 56025, Italy; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, 14496-14535, Iran.
| | - Matineh Ghomi
- Chemistry Department, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, 6153753843, Iran
| | - Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, 51666-16471, Iran
| | - Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, Białystok, 15-089, Poland
| | - Tarun Agarwal
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, 721302, India
| | - Masoud Delfi
- Department of Chemical Sciences, University of Naples "Federico II", Naples, 80126, Italy
| | - Javad Akhtari
- Toxoplasmosis Research Center, Communicable Diseases Institute, Department of Medical Nanotechnology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Vinod V T Padil
- Department of Nanomaterials in Natural Sciences, Institute for Nanomaterials, Advanced Technologies and Innovation (CXI), Technical University of Liberec (TUL), Studentská, 1402/2, Liberec, Czech Republic
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul, 34956, Turkey; Center of Excellence for Functional Surfaces and Interfaces (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, 34956, Turkey
| | - Nahid Pourreza
- Chemistry Department, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, 6153753843, Iran
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, Białystok, 15-089, Poland
| | - Tapas Kumar Maiti
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, 721302, India
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19
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Lorch U, Pierscionek T, Freier A, Spencer CS, Täubel J. Safety, Tolerability, and Dose Proportionality of a Novel Transdermal Fentanyl Matrix Patch and Bioequivalence With a Matrix Fentanyl Patch: Two Phase 1 Single-Center Open-Label, Randomized Crossover Studies in Healthy Japanese Volunteers. Clin Pharmacol Drug Dev 2020; 10:260-271. [PMID: 32748570 PMCID: PMC7984375 DOI: 10.1002/cpdd.846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/07/2020] [Indexed: 11/29/2022]
Abstract
Two open‐label, single‐dose, randomized crossover studies were conducted in healthy Japanesemen to (1) assess dose proportionality of 5 doses (1.38, 2.75, 5.5, 8.25, and 11.0 mg) of Lafenta, a novel matrix‐type transdermal fentanyl patch with a rate‐controlling membrane; and (2) compare patch bioequivalence (11.0 mg) with a commercially available reference patch (Durotep MT Patch [16.8 mg]). Pharmacokinetics, adhesion performance, residual fentanyl, and safety parameters were assessed. Increases in mean AUC0‐t and Cmax after application of the test patch were dose proportional. The test patch (11.0 mg) was bioequivalent to the 16.8‐mg reference patch in terms of mean AUC0‐inf, AUC0‐t, and Cmax. Residual fentanyl levels 72 hours postapplication were lower in the test than in the reference patch. Differences in adhesion performance between the test and the reference patch did not affect delivery efficacy and reliability of the novel matrix patch. Safety findings were in line with previous experiences with fentanyl. Both studies showed low variation in fentanyl exposure and delivery via the test patch. The test patch provided equivalent fentanyl exposure at a lower dose than the reference patch formulation with lower variability and the potential to lower medicinal waste.
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Affiliation(s)
- Ulrike Lorch
- Richmond Pharmacology Ltd., St George's University London, London, UK
| | | | | | | | - Jörg Täubel
- Richmond Pharmacology Ltd., St George's University London, London, UK.,St George's University London, London, UK
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20
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Almeman AA. Major CYP450 polymorphism Among Saudi Patients. Drug Metab Lett 2020; 14:17-24. [PMID: 32703145 DOI: 10.2174/1872312814666200722122232] [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: 03/28/2020] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND Cytochrome P450 (CYP) contributes to a huge collection of medicinal products' Phase I metabolization. We aimed to summarize and investigate the current evidence regarding the frequency of CYP2D6, CYP2C9, CYP2C19, MDR1 in Saudi Arabia. METHODS A computerized search in four databases was done using the relevant keywords. Screening process was done in two steps; title and abstract screening and full-text screening. Data of demographic and characteristics of included studies and patients was extracted and tabulated. RESULTS Ten studies were eligible for our criteria and were included in this systematic review. Age of participants ranged between 17-65 years. Only two subjects showed PM phenotype of CYP2C19 in Saudi population. The most frequent alleles were CYP2C19*1 (62.9%), CYP2C19*2 (11.2%-32%), and CYP2C19*17 (25.7%). The CYP2C19m1 was observed in 97 cases of extensive metabolizing (EM) phenotype CYP2C19. Concerning the CYP2C9, the most frequent alleles were CYP2C9*1 and CYP2C9*2, and the most frequent genotype was CYP2C9*1*1. The CYP2D6*41 allele and C1236T MDR1 were the most frequent allele in this population. CONCLUSION The current evidence suggests that Saudi Arabians resembled European in the frequency of CYP2C19, Caucasians in both the incidence of CYP2C9 and CYP2C19m1 and absence of CYP2C19m2. The CYP2D6*41 allele frequency in Saudi Arabians is relatively high. We recommend a further research to evaluate the basic and clinical relevance of gene polymorphism in such ethnicity.
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Affiliation(s)
- Ahmad Abdulrahman Almeman
- Clinical pharmacology and therapeutics Department, Qassim University, Buraydah, Qassim. Saudi Arabia
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21
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Mallah N, Zapata-Cachafeiro M, Aguirre C, Ibarra-García E, Palacios-Zabalza I, Macías-García F, Domínguez-Muñoz JE, Piñeiro-Lamas M, Ibáñez L, Vidal X, Vendrell L, Martin-Arias L, Sáinz-Gil M, Velasco-González V, Figueiras A. Influence of Polymorphisms Involved in Platelet Activation and Inflammatory Response on Aspirin-Related Upper Gastrointestinal Bleeding: A Case-Control Study. Front Pharmacol 2020; 11:860. [PMID: 32655394 PMCID: PMC7325915 DOI: 10.3389/fphar.2020.00860] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022] Open
Abstract
Background Despite the wide benefits of aspirin and its cost-effectiveness, aspirin prescriptions have been reduced due to idiosyncratic responses in susceptible individuals. Low-dose aspirin and single-nucleotide polymorphisms (SNPs) are independently associated with increased risk of gastrointestinal hemorrhage; however, to-date, no studies investigated the SNP-aspirin interaction effect on upper gastrointestinal hemorrhage (UGIH). Therefore, we aimed to evaluate the role of 25 SNPs in multiple genes involved in platelet activation, angiogenesis and inflammatory response in aspirin-related UGIH. Methods A multicenter, full case–control study was conducted in patients exposed and unexposed to aspirin. Three hundred twenty-six cases diagnosed with UGIH were matched with 748 controls (1:3) by age, gender, health center, and recruitment date. Only adults of European origin were included. Participants were stratified by aspirin exposure and genotype [(Aspirin(−), wild-type), (Aspirin(+), wild-type), (Aspirin(+), genetic variation), (Aspirin(−), genetic variation)]. For each SNP, the Odds Ratio of UGIH and their 95% confidence intervals were estimated in each subgroup by using the generalized linear mixed models for dependent binomial variables. SNP-aspirin interaction effect was estimated through Relative Excess Risk due to Interaction (RERI) measures. Results We observed two categories of SNPs that might modify the risk magnitude of UGIH in aspirin consumers. Seven SNPs (rs1387180 A > G, rs2238631 T > C, rs1799964 T > C, rs5050 T > C/T > G, rs689466 T > C, rs1799983 T > A/T > G, and rs7756935 C > A) were “positive modifiers” associated with an excess of risk from aspirin exposure and carrying that genetic variation (1.75 ≤ RERI ≤ 4.95). On the contrary, the following nine SNPs (rs2243086 G > T, rs1131882 G > A, rs4311994 C > T, rs10120688 G > A, rs4251961 T > C, rs3778355 G > C, rs1330344 C > T, rs5275 A > G/A > T, and rs3779647 C > T) were “negative modifiers” and associated with a reduced risk in aspirin users (−2.74 ≤ RERI ≤ −0.95). Conclusion This preliminary study suggests that polymorphisms in genes involved in platelets activity, angiogenesis and inflammatory response might modify the risk of aspirin-related UGIH. Further studies with larger sample size and in different populations are needed to confirm our findings. If confirmed, this might have great impact on public health, thanks to aspirin’s prophylactic properties in diseases of high incidence and severity.
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Affiliation(s)
- Narmeen Mallah
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain.,Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública - CIBERESP), Carlos III Health Institute, Madrid, Spain
| | - Maruxa Zapata-Cachafeiro
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain.,Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública - CIBERESP), Carlos III Health Institute, Madrid, Spain
| | - Carmelo Aguirre
- Biocruces Bizkaia Health Research Institute, Pharmacotherapy Group, Bizkaia, Spain.,University Hospital of Galdakao-Usansolo. Basque Country Pharmacovigilance Unit, Osakidetza, Spain.,Pharmacology Department, Medicine and Nursing Faculty, University of the Basque Country, Barakaldo, Bizkaia, Spain
| | - Eguzkiñe Ibarra-García
- Biocruces Bizkaia Health Research Institute, Pharmacotherapy Group, Bizkaia, Spain.,Osakidetza Basque Health Service, Urduliz Hospital, Pharmacy Department, Urduliz, Spain
| | - Itziar Palacios-Zabalza
- Biocruces Bizkaia Health Research Institute, Pharmacotherapy Group, Bizkaia, Spain.,University Hospital of Galdakao-Usansolo. Basque Country Pharmacovigilance Unit, Osakidetza, Spain
| | - Fernando Macías-García
- Department of Gastroenterology and Hepatology, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - J Enrique Domínguez-Muñoz
- Department of Gastroenterology and Hepatology, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - María Piñeiro-Lamas
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública - CIBERESP), Carlos III Health Institute, Madrid, Spain.,Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Luisa Ibáñez
- Department of Pharmacology, Therapeutics and Toxicology, Catalonian Institute of Pharmacology, Clinical Pharmacology Service, Vall d'Hebron University Teaching Hospital, Autonomous University, Barcelona, Spain
| | - Xavier Vidal
- Department of Pharmacology, Therapeutics and Toxicology, Catalonian Institute of Pharmacology, Clinical Pharmacology Service, Vall d'Hebron University Teaching Hospital, Autonomous University, Barcelona, Spain
| | - Lourdes Vendrell
- Department of Pharmacology, Therapeutics and Toxicology, Catalonian Institute of Pharmacology, Clinical Pharmacology Service, Vall d'Hebron University Teaching Hospital, Autonomous University, Barcelona, Spain
| | - Luis Martin-Arias
- Centre for Research on Drug Safety (CESME), Valladolid University, Valladolid, Spain
| | - María Sáinz-Gil
- Centre for Research on Drug Safety (CESME), Valladolid University, Valladolid, Spain
| | | | - Adolfo Figueiras
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain.,Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública - CIBERESP), Carlos III Health Institute, Madrid, Spain.,Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
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22
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Towards precision medicine: interrogating the human genome to identify drug pathways associated with potentially functional, population-differentiated polymorphisms. THE PHARMACOGENOMICS JOURNAL 2019; 19:516-527. [PMID: 31578463 PMCID: PMC6867962 DOI: 10.1038/s41397-019-0096-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/10/2019] [Accepted: 09/18/2019] [Indexed: 12/24/2022]
Abstract
Drug response variations amongst different individuals/populations are influenced by several factors including allele frequency differences of single nucleotide polymorphisms (SNPs) that functionally affect drug-response genes. Here, we aim to identify drugs that potentially exhibit population differences in response using SNP data mining and analytics. Ninety-one pairwise-comparisons of >22,000,000 SNPs from the 1000 Genomes Project, across 14 different populations, were performed to identify ‘population-differentiated’ SNPs (pdSNPs). Potentially-functional pdSNPs (pf-pdSNPs) were then selected, mapped into genes, and integrated with drug–gene databases to identify ‘population-differentiated’ drugs enriched with genes carrying pf-pdSNPs. 1191 clinically-approved drugs were found to be significantly enriched (Z > 2.58) with genes carrying SNPs that were differentiated in one or more population-pair comparisons. Thirteen drugs were found to be enriched with such differentiated genes across all 91 population-pairs. Notably, 82% of drugs, which were previously reported in the literature to exhibit population differences in response were also found by this method to contain a significant enrichment of population specific differentiated SNPs. Furthermore, drugs with genetic testing labels, or those suspected to cause adverse reactions, contained a significantly larger number (P < 0.01) of population-pairs with enriched pf-pdSNPs compared with those without these labels. This pioneering effort at harnessing big-data pharmacogenomics to identify ‘population differentiated’ drugs could help to facilitate data-driven decision-making for a more personalized medicine.
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23
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Choi YH, Han CY, Kim KS, Kim SG. Future Directions of Pharmacovigilance Studies Using Electronic Medical Recording and Human Genetic Databases. Toxicol Res 2019; 35:319-330. [PMID: 31636843 PMCID: PMC6791658 DOI: 10.5487/tr.2019.35.4.319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/25/2019] [Accepted: 05/08/2019] [Indexed: 12/11/2022] Open
Abstract
Adverse drug reactions (ADRs) constitute key factors in determining successful medication therapy in clinical situations. Integrative analysis of electronic medical record (EMR) data and use of proper analytical tools are requisite to conduct retrospective surveillance of clinical decisions on medications. Thus, we suggest that electronic medical recording and human genetic databases are considered together in future directions of pharmacovigilance. We analyzed EMR-based ADR studies indexed on PubMed during the period from 2005 to 2017 and retrospectively acquired 1161 (29.6%) articles describing drug-induced adverse reactions (e.g., liver, kidney, nervous system, immune system, and inflammatory responses). Of them, only 102 (8.79%) articles contained useful information to detect or predict ADRs in the context of clinical medication alerts. Since insufficiency of EMR datasets and their improper analyses may provide false warnings on clinical decision, efforts should be made to overcome possible problems on data-mining, analysis, statistics, and standardization. Thus, we address the characteristics and limitations on retrospective EMR database studies in hospital settings. Since gene expression and genetic variations among individuals impact ADRs, pharmacokinetics, and pharmacodynamics, appropriate paths for pharmacovigilance may be optimized using suitable databases available in public domain (e.g., genome-wide association studies (GWAS), non-coding RNAs, microRNAs, proteomics, and genetic variations), novel targets, and biomarkers. These efforts with new validated biomarker analyses would be of help to repurpose clinical and translational research infrastructure and ultimately future personalized therapy considering ADRs.
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Affiliation(s)
- Young Hee Choi
- College of Pharmacy, Dongguk University_Seoul, Goyang,
Korea
| | - Chang Yeob Han
- Department of Pharmacology, School of Medicine, Wonkwang University, Iksan,
Korea
| | - Kwi Suk Kim
- Department of Pharmacy, Seoul National University Hospital, Seoul,
Korea
| | - Sang Geon Kim
- Department of Pharmacy, Seoul National University Hospital, Seoul,
Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul,
Korea
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24
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Rohde PD, Jensen IR, Sarup PM, Ørsted M, Demontis D, Sørensen P, Kristensen TN. Genetic Signatures of Drug Response Variability in Drosophila melanogaster. Genetics 2019; 213:633-650. [PMID: 31455722 PMCID: PMC6781897 DOI: 10.1534/genetics.119.302381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/26/2019] [Indexed: 12/27/2022] Open
Abstract
Knowledge of the genetic basis underlying variation in response to environmental exposures or treatments is important in many research areas. For example, knowing the set of causal genetic variants for drug responses could revolutionize personalized medicine. We used Drosophila melanogaster to investigate the genetic signature underlying behavioral variability in response to methylphenidate (MPH), a drug used in the treatment of attention-deficit/hyperactivity disorder. We exposed a wild-type D. melanogaster population to MPH and a control treatment, and observed an increase in locomotor activity in MPH-exposed individuals. Whole-genome transcriptomic analyses revealed that the behavioral response to MPH was associated with abundant gene expression alterations. To confirm these patterns in a different genetic background and to further advance knowledge on the genetic signature of drug response variability, we used a system of inbred lines, the Drosophila Genetic Reference Panel (DGRP). Based on the DGRP, we showed that the behavioral response to MPH was strongly genotype-dependent. Using an integrative genomic approach, we incorporated known gene interactions into the genomic analyses of the DGRP, and identified putative candidate genes for variability in drug response. We successfully validated 71% of the investigated candidate genes by gene expression knockdown. Furthermore, we showed that MPH has cross-generational behavioral and transcriptomic effects. Our findings establish a foundation for understanding the genetic mechanisms driving genotype-specific responses to medical treatment, and highlight the opportunities that integrative genomic approaches have in optimizing medical treatment of complex diseases.
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Affiliation(s)
- Palle Duun Rohde
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus C, Denmark
- Center for Integrative Sequencing, Aarhus University, 8000, Denmark
| | - Iben Ravnborg Jensen
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
| | - Pernille Merete Sarup
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Michael Ørsted
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus C, Denmark
- Center for Integrative Sequencing, Aarhus University, 8000, Denmark
- Department of Biomedicine, Aarhus University, 8000, Denmark
| | - Peter Sørensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Torsten Nygaard Kristensen
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
- Section for Genetics, Ecology and Evolution, Department of Bioscience, Aarhus University, 8000, Denmark
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25
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Abstract
Next-generation sequencing (NGS) data have been central to the development of targeted therapy and immunotherapy for precision oncology. In targeted therapy, drugs directly attack cancer, by altering the expression of critical cancer genes identified with cancer genome profiling. Immunotherapy drugs indirectly attack cancer, by inducing the immune system to attack and treat cancer. Harnessing genomic data for deployment and development of immunotherapy comprises the field of immunogenomics. The discovery of a link between cancer cells escaping immune destruction and cancer progression, led to extensive research into this mechanism and drug development. In the past few years, FDA has granted accelerated approval to several immunotherapy cancer treatment drugs, pembrolizumab, nivolumab, and atezolizumab, belonging to the class of checkpoint inhibitors. Utilization of pretreatment genomic cancer screening to identify patients most likely to respond to immunotherapy and to customize immunotherapy for a given patient, promises to improve cancer treatment outcomes. Recent advances in molecular profiling, high-throughput sequencing, and computational efficiency has made immunogenomics the major tenet of precision medicine in cancer treatment. This review provides a brief overview on the state of art of immunogenomics in precision cancer medicine.
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26
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Bolaji OO, Adehin A, Adeagbo BA. Pharmacogenomics in the Nigerian population: the past, the present and the future. Pharmacogenomics 2019; 20:915-926. [DOI: 10.2217/pgs-2019-0046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Nigerian population exhibits huge ethnic and genetic diversity, typical of African populations, which can be harnessed for improved drug-response and disease management. Existing data on genes relevant to drug response, so far generated for the population, indeed confirm the prevalence of some clinically significant pharmacogenes. These reports detail prevailing genetic alleles and metabolic phenotypes of vital drug metabolizing monooxygenases, transferases and drug transporters. While the utilization of existing pharmacogenomic data for healthcare delivery remains unpopular, several past and on-going studies suggest that a future shift toward genotype-stratified dosing of drugs and disease management in the population is imminent. This review discusses the present state of pharmacogenomics in Nigeria and the potential benefits of sustained research in this field for the population.
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Affiliation(s)
- Oluseye O Bolaji
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Ayorinde Adehin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
- Institute of Biomedical & Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, PR China
| | - Babatunde A Adeagbo
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
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27
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Majoros WH, Kim YS, Barrera A, Li F, Wang X, Cunningham SJ, Johnson GD, Guo C, Lowe WL, Scholtens DM, Hayes MG, Reddy TE, Allen AS. Bayesian estimation of genetic regulatory effects in high-throughput reporter assays. Bioinformatics 2019; 36:331-338. [PMID: 31368479 PMCID: PMC7999138 DOI: 10.1093/bioinformatics/btz545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 06/12/2019] [Accepted: 07/24/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION High-throughput reporter assays dramatically improve our ability to assign function to noncoding genetic variants, by measuring allelic effects on gene expression in the controlled setting of a reporter gene. Unlike genetic association tests, such assays are not confounded by linkage disequilibrium when loci are independently assayed. These methods can thus improve the identification of causal disease mutations. While work continues on improving experimental aspects of these assays, less effort has gone into developing methods for assessing the statistical significance of assay results, particularly in the case of rare variants captured from patient DNA. RESULTS We describe a Bayesian hierarchical model, called Bayesian Inference of Regulatory Differences, which integrates prior information and explicitly accounts for variability between experimental replicates. The model produces substantially more accurate predictions than existing methods when allele frequencies are low, which is of clear advantage in the search for disease-causing variants in DNA captured from patient cohorts. Using the model, we demonstrate a clear tradeoff between variant sequencing coverage and numbers of biological replicates, and we show that the use of additional biological replicates decreases variance in estimates of effect size, due to the properties of the Poisson-binomial distribution. We also provide a power and sample size calculator, which facilitates decision making in experimental design parameters. AVAILABILITY AND IMPLEMENTATION The software is freely available from www.geneprediction.org/bird. The experimental design web tool can be accessed at http://67.159.92.22:8080. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- William H Majoros
- Duke Center for Statistical Genetics and Genomics, Duke University,Division of Integrative Genomics, Department of Biostatistics and Bioinformatics, Duke University Medical School,Center for Genomic and Computational Biology, Duke University Medical School
| | - Young-Sook Kim
- Center for Genomic and Computational Biology, Duke University Medical School,Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27710
| | - Alejandro Barrera
- Center for Genomic and Computational Biology, Duke University Medical School
| | - Fan Li
- Department of Biostatistics, Yale University, New Haven, CT 06520
| | - Xingyan Wang
- Present address: PhD Program in Biostatistics, Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA
| | | | - Graham D Johnson
- Center for Genomic and Computational Biology, Duke University Medical School,Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710
| | - Cong Guo
- Present address: Human Genetics, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - William L Lowe
- Division of Endocrinology Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago
| | - Denise M Scholtens
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - M Geoffrey Hayes
- Division of Endocrinology Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago
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28
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Richards J, Tang S, Gunsch G, Sul P, Wiet M, Flanigan DC, Khan SN, Moore S, Walter B, Purmessur D. Mast Cell/Proteinase Activated Receptor 2 (PAR2) Mediated Interactions in the Pathogenesis of Discogenic Back Pain. Front Cell Neurosci 2019; 13:294. [PMID: 31333416 PMCID: PMC6625229 DOI: 10.3389/fncel.2019.00294] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/17/2019] [Indexed: 12/19/2022] Open
Abstract
Mast cells (MCs) are present in the painful degenerate human intervertebral disc (IVD) and are associated with disease pathogenesis. MCs release granules containing enzymatic and inflammatory factors in response to stimulants or allergens. The serine protease, tryptase, is unique to MCs and its activation of the G-protein coupled receptor, Protease Activated Receptor 2 (PAR2), induces inflammation and degradation in osteoarthritic cartilage. Our previously published work has demonstrated increased levels of MC marker tryptase in IVD samples from discogenic back pain patients compared to healthy control IVD samples including expression of chemotactic agents that may facilitate MC migration into the IVD. To further elucidate MCs’ role in the IVD and mechanisms underlying its effects, we investigated whether (1) human IVD cells can promote MC migration, (2) MC tryptase can mediate up-regulation of inflammatory/catabolic process in human IVD cells and tissue, and (3) the potential of PAR2 antagonist to function as a therapeutic drug in in vitro human and ex vivo bovine pilot models of disease. MC migration was quantitatively assessed using conditioned media from primary human IVD cells and MC migration examined through Matrigel. Exposure to soluble IVD factors significantly enhanced MC migration, suggesting IVD cells can recruit MCs. We also demonstrated significant upregulation of MC chemokine SCF and angiogenic factor VEGFA gene expression in human IVD cells in vitro in response to recombinant human tryptase, suggesting tryptase can enhance recruitment of MCs and promotion of angiogenesis into the usually avascular IVD. Furthermore, tryptase can degrade proteoglycans in IVD tissue as demonstrated by significant increases in glycosaminoglycans released into surrounding media. This can create a catabolic microenvironment compromising structural integrity and facilitating vascular migration usually inhibited by the anti-angiogenic IVD matrix. Finally, as a “proof of concept” study, we examined the therapeutic potential of PAR2 antagonist (PAR2A) on human IVD cells and bovine organ culture IVD model. While preliminary data shows promise and points toward structural restoration of the bovine IVD including down-regulation of VEGFA, effects of PAR2 antagonist on human IVD cells differ between gender and donors suggesting that further validation is required with larger cohorts of human specimens.
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Affiliation(s)
- Justin Richards
- College of Arts and Sciences, The Ohio State University, Columbus, OH, United States
| | - Shirley Tang
- College of Engineering, The Ohio State University, Columbus, OH, United States
| | - Gilian Gunsch
- College of Arts and Sciences, The Ohio State University, Columbus, OH, United States
| | - Pavel Sul
- College of Engineering, The Ohio State University, Columbus, OH, United States
| | - Matthew Wiet
- College of Engineering, The Ohio State University, Columbus, OH, United States
| | - David C Flanigan
- Department of Orthopaedics, Wexner Medical Center, The Ohio State University, Columbus, OH, United States
| | - Safdar N Khan
- Department of Orthopaedics, Wexner Medical Center, The Ohio State University, Columbus, OH, United States
| | - Sarah Moore
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, United States
| | - Benjamin Walter
- College of Engineering, The Ohio State University, Columbus, OH, United States.,Department of Orthopaedics, Wexner Medical Center, The Ohio State University, Columbus, OH, United States
| | - Devina Purmessur
- College of Engineering, The Ohio State University, Columbus, OH, United States.,Department of Orthopaedics, Wexner Medical Center, The Ohio State University, Columbus, OH, United States
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29
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Pharmacogenomics-based practice in North Cyprus: its adoption by pharmacists and their attitudes and knowledge. Int J Clin Pharm 2019; 41:1299-1306. [PMID: 31267362 DOI: 10.1007/s11096-019-00868-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 06/20/2019] [Indexed: 12/22/2022]
Abstract
Background Pharmacogenomics is a branch of biotechnological science integrating medicine, pharmacology, and genomics techniques. Moreover, it focuses on creating drug therapies in order to analyze genetic differences in patients causing various responses to a single therapeutic regimen. Objective This cross sectional study aimed to examine the attitude, knowledge and adoption among pharmacists in North Cyprus and the most appropriate method to improve education among them. Setting Community pharmacy setting. Method A total of 103 out of 140 pharmacists responded to a pre-tested and validated questionnaire consisting of 25 items during July through September 2016. Main outcome measure Pharmacists attitude, knowledge and adoption towards pharmacogenomic tests. Result Data showed that most of the pharmacists in North Cyprus had positive attitude and knowledge scores with mean value of 28.3 ± 5.3 (out of 40) and 6.9 ± 0.8 (out of 10) respectively, further findings showed that there is a significant difference among age groups in their total attitude score (p < 0.05). Conclusion Even though pharmacogenomics is a field promising a variety of benefits, it is vital to implement it in clinical settings in order to improve outcomes. Our findings highlight the necessity for more education on the availability and interpretation of pharmacogenomics tests.
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30
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Wang B, Yan C, Lou S, Emani P, Li B, Xu M, Kong X, Meyerson W, Yang YT, Lee D, Gerstein M. Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions. Structure 2019; 27:1469-1481.e3. [PMID: 31279629 DOI: 10.1016/j.str.2019.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 02/14/2019] [Accepted: 06/03/2019] [Indexed: 11/17/2022]
Abstract
A key issue in drug design is how population variation affects drug efficacy by altering binding affinity (BA) in different individuals, an essential consideration for government regulators. Ideally, we would like to evaluate the BA perturbations of millions of single-nucleotide variants (SNVs). However, only hundreds of protein-drug complexes with SNVs have experimentally characterized BAs, constituting too small a gold standard for straightforward statistical model training. Thus, we take a hybrid approach: using physically based calculations to bootstrap the parameterization of a full model. In particular, we do 3D structure-based docking on ∼10,000 SNVs modifying known protein-drug complexes to construct a pseudo gold standard. Then we use this augmented set of BAs to train a statistical model combining structure, ligand and sequence features and illustrate how it can be applied to millions of SNVs. Finally, we show that our model has good cross-validated performance (97% AUROC) and can also be validated by orthogonal ligand-binding data.
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Affiliation(s)
- Bo Wang
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Chengfei Yan
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Prashant Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Bian Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Min Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Xiangmeng Kong
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - William Meyerson
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Yale School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Yucheng T Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Donghoon Lee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA.
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31
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Oulas A, Minadakis G, Zachariou M, Sokratous K, Bourdakou MM, Spyrou GM. Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. Brief Bioinform 2019; 20:806-824. [PMID: 29186305 PMCID: PMC6585387 DOI: 10.1093/bib/bbx151] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/17/2017] [Indexed: 02/01/2023] Open
Abstract
Systems Bioinformatics is a relatively new approach, which lies in the intersection of systems biology and classical bioinformatics. It focuses on integrating information across different levels using a bottom-up approach as in systems biology with a data-driven top-down approach as in bioinformatics. The advent of omics technologies has provided the stepping-stone for the emergence of Systems Bioinformatics. These technologies provide a spectrum of information ranging from genomics, transcriptomics and proteomics to epigenomics, pharmacogenomics, metagenomics and metabolomics. Systems Bioinformatics is the framework in which systems approaches are applied to such data, setting the level of resolution as well as the boundary of the system of interest and studying the emerging properties of the system as a whole rather than the sum of the properties derived from the system's individual components. A key approach in Systems Bioinformatics is the construction of multiple networks representing each level of the omics spectrum and their integration in a layered network that exchanges information within and between layers. Here, we provide evidence on how Systems Bioinformatics enhances computational therapeutics and diagnostics, hence paving the way to precision medicine. The aim of this review is to familiarize the reader with the emerging field of Systems Bioinformatics and to provide a comprehensive overview of its current state-of-the-art methods and technologies. Moreover, we provide examples of success stories and case studies that utilize such methods and tools to significantly advance research in the fields of systems biology and systems medicine.
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Affiliation(s)
- Anastasis Oulas
- Bioinformatics European Research Area Chair, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George Minadakis
- Bioinformatics European Research Area Chair, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Margarita Zachariou
- Bioinformatics European Research Area Chair, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kleitos Sokratous
- Bioinformatics European Research Area Chair, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marilena M Bourdakou
- Bioinformatics European Research Area Chair, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M Spyrou
- Bioinformatics European Research Area Chair, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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Schwarz UI, Gulilat M, Kim RB. The Role of Next-Generation Sequencing in Pharmacogenetics and Pharmacogenomics. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a033027. [PMID: 29844222 DOI: 10.1101/cshperspect.a033027] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Inherited genetic variations in pharmacogenetic loci are widely acknowledged as important determinants of phenotypic differences in drug response, and may be actionable in the clinic. However, recent studies suggest that a considerable number of novel rare variants in pharmacogenes likely contribute to a still unexplained fraction of the observed interindividual variability. Next-generation sequencing (NGS) represents a rapid, relatively inexpensive, large-scale DNA sequencing technology with potential relevance as a comprehensive pharmacogenetic genotyping platform to identify genetic variation related to drug therapy. However, many obstacles remain before the clinical use of NGS-based test results, including technical challenges, functional interpretation, and strict requirements for diagnostic tests. Advanced computational analyses, high-throughput screening methodologies, and generation of shared resources with cell-based and clinical information will facilitate the integration of NGS data into candidate genotyping approaches, likely enhancing future drug phenotype predictions in patients.
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Affiliation(s)
- Ute I Schwarz
- Division of Clinical Pharmacology, Department of Medicine, Western University, London, Ontario N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, London, Ontario N6A 5A5, Canada
| | - Markus Gulilat
- Department of Physiology and Pharmacology, Western University, London, Ontario N6A 5A5, Canada
| | - Richard B Kim
- Division of Clinical Pharmacology, Department of Medicine, Western University, London, Ontario N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, London, Ontario N6A 5A5, Canada
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Najafipour M, Zareizadeh M, Khokhi MA, Najafipour F. Comparative study of the effect of atorvastatin and fenofibrate on high-density lipoprotein cholesterol levels in patients with type 2 diabetes. J Adv Pharm Technol Res 2019; 9:135-138. [PMID: 30637231 PMCID: PMC6302688 DOI: 10.4103/japtr.japtr_314_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Diabetes is the most common metabolic disease. Type 2 diabetes is a variable combination of insulin resistance and disorder in insulin secretion, leading to disorder of lipids and plasma lipoproteins. The most common pattern of dyslipidemia in diabetic is high triglyceride (TG) and low high-density lipoprotein cholesterol (HDL-C). This study was conducted to find a more effective drug to increase HDL-C. In this study, 80 patients (26 males and 54 females) with type 2 diabetes received fenofibrate in cross-sectional way for 2 months, and they did not take antilipid drugs for 2 month. Then, they underwent atorvastatin for 2 months and HDL-C was measured before and after taking drugs. Patients did not change their diet during this study. Effect of atorvastatin and fenofibrate on HDL-C levels in patients with type 2 diabetes was evaluated. The mean HDL-C and total cholesterol (TC) before and after taking drugs were 36.5 mg/dL and 174.56 mg/dL, respectively. After atorvastatin, the mean HDL-C and TC were 43.30 and 150.144 mg/dL, respectively, and after fenofibrate, 43.40 were mg/dL and 146.36 mg/dL, respectively. Atorvastatin caused increase in HDL-C by 18.44% and reduction in TC by 13.82% and fenofibrate increase in HDL-C by18.62% and reduction in TC by 16.05%. No difference was seen between atorvastatin and fenofibrate in terms of effect on the HDL-C excess (P = 0.449). In addition, no difference was seen between atorvastatin and fenofibrate in terms of effect on TC reduction (P = 0.992). In conclusion various factors are involved in increasing the HDL, such as race, sex, nutrition, physical activity and, of course, medications. The effect of medications is also different on races and genetics. The value of increase in HDL-C after Fenofibrate and Atorvastatin was associated with gender so that it caused more increase of HDL-C in females.
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Affiliation(s)
- Mostafa Najafipour
- Young Researchers and Elite Club, Ardabil Branch, Islamic Azad University, Ardabil, Iran.,Department of Endocrinology, Faculty of Medicine, Azad Ardabil University of Medical Sciences, Ardabil, Iran
| | - Masoumeh Zareizadeh
- Endocrine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Farzad Najafipour
- Endocrine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Piñero J, Gonzalez-Perez A, Guney E, Aguirre-Plans J, Sanz F, Oliva B, Furlong LI. Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response. Front Genet 2018; 9:412. [PMID: 30319692 PMCID: PMC6168038 DOI: 10.3389/fgene.2018.00412] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/05/2018] [Indexed: 11/13/2022] Open
Abstract
Understanding the mechanisms underlying drug therapeutic action and toxicity is crucial for the prevention and management of drug adverse reactions, and paves the way for a more efficient and rational drug design. The characterization of drug targets, drug metabolism proteins, and proteins associated to side effects according to their expression patterns, their tolerance to genomic variation and their role in cellular networks, is a necessary step in this direction. In this contribution, we hypothesize that different classes of proteins involved in the therapeutic effect of drugs and in their adverse effects have distinctive transcriptomics, genomics and network features. We explored the properties of these proteins within global and organ-specific interactomes, using multi-scale network features, evaluated their gene expression profiles in different organs and tissues, and assessed their tolerance to loss-of-function variants leveraging data from 60K subjects. We found that drug targets that mediate side effects are more central in cellular networks, more intolerant to loss-of-function variation, and show a wider breadth of tissue expression than targets not mediating side effects. In contrast, drug metabolizing enzymes and transporters are less central in the interactome, more tolerant to deleterious variants, and are more constrained in their tissue expression pattern. Our findings highlight distinctive features of proteins related to drug action, which could be applied to prioritize drugs with fewer probabilities of causing side effects.
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Affiliation(s)
- Janet Piñero
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Emre Guney
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Joaquim Aguirre-Plans
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ferran Sanz
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Baldo Oliva
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Laura I Furlong
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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Hanson C, Cairns J, Wang L, Sinha S. Principled multi-omic analysis reveals gene regulatory mechanisms of phenotype variation. Genome Res 2018; 28:1207-1216. [PMID: 29898900 PMCID: PMC6071639 DOI: 10.1101/gr.227066.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 05/31/2018] [Indexed: 12/12/2022]
Abstract
Recent studies have analyzed large-scale data sets of gene expression to identify genes associated with interindividual variation in phenotypes ranging from cancer subtypes to drug sensitivity, promising new avenues of research in personalized medicine. However, gene expression data alone is limited in its ability to reveal cis-regulatory mechanisms underlying phenotypic differences. In this study, we develop a new probabilistic model, called pGENMi, that integrates multi-omic data to investigate the transcriptional regulatory mechanisms underlying interindividual variation of a specific phenotype—that of cell line response to cytotoxic treatment. In particular, pGENMi simultaneously analyzes genotype, DNA methylation, gene expression, and transcription factor (TF)-DNA binding data, along with phenotypic measurements, to identify TFs regulating the phenotype. It does so by combining statistical information about expression quantitative trait loci (eQTLs) and expression-correlated methylation marks (eQTMs) located within TF binding sites, as well as observed correlations between gene expression and phenotype variation. Application of pGENMi to data from a panel of lymphoblastoid cell lines treated with 24 drugs, in conjunction with ENCODE TF ChIP data, yielded a number of known as well as novel (TF, Drug) associations. Experimental validations by TF knockdown confirmed 41% of the predicted and tested associations, compared to a 12% confirmation rate of tested nonassociations (controls). An extensive literature survey also corroborated 62% of the predicted associations above a stringent threshold. Moreover, associations predicted only when combining eQTL and eQTM data showed higher precision compared to an eQTL-only or eQTM-only analysis using pGENMi, further demonstrating the value of multi-omic integrative analysis.
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Affiliation(s)
- Casey Hanson
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Junmei Cairns
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Saurabh Sinha
- Department of Computer Science and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Doestzada M, Vila AV, Zhernakova A, Koonen DPY, Weersma RK, Touw DJ, Kuipers F, Wijmenga C, Fu J. Pharmacomicrobiomics: a novel route towards personalized medicine? Protein Cell 2018; 9:432-445. [PMID: 29705929 PMCID: PMC5960471 DOI: 10.1007/s13238-018-0547-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/16/2018] [Indexed: 02/06/2023] Open
Abstract
Inter-individual heterogeneity in drug response is a serious problem that affects the patient's wellbeing and poses enormous clinical and financial burdens on a societal level. Pharmacogenomics has been at the forefront of research into the impact of individual genetic background on drug response variability or drug toxicity, and recently the gut microbiome, which has also been called the second genome, has been recognized as an important player in this respect. Moreover, the microbiome is a very attractive target for improving drug efficacy and safety due to the opportunities to manipulate its composition. Pharmacomicrobiomics is an emerging field that investigates the interplay of microbiome variation and drugs response and disposition (absorption, distribution, metabolism and excretion). In this review, we provide a historical overview and examine current state-of-the-art knowledge on the complex interactions between gut microbiome, host and drugs. We argue that combining pharmacogenomics and pharmacomicrobiomics will provide an important foundation for making major advances in personalized medicine.
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Affiliation(s)
- Marwah Doestzada
- Departments of Genetics, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
- Departments of Paediatrics, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Arnau Vich Vila
- Departments of Genetics, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
- Departments of Gastroenterology & Hepatology, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Departments of Genetics, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Debby P Y Koonen
- Departments of Paediatrics, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Rinse K Weersma
- Departments of Gastroenterology & Hepatology, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Daan J Touw
- Departments of Clinical Pharmacy & Pharmacology, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Folkert Kuipers
- Departments of Paediatrics, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
- Departments of Laboratory Medicine, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cisca Wijmenga
- Departments of Genetics, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, P.O. Box 1072, Blindern, 0316, Oslo, Norway
| | - Jingyuan Fu
- Departments of Genetics, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands.
- Departments of Paediatrics, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands.
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Schärfe CPI, Tremmel R, Schwab M, Kohlbacher O, Marks DS. Genetic variation in human drug-related genes. Genome Med 2017; 9:117. [PMID: 29273096 PMCID: PMC5740940 DOI: 10.1186/s13073-017-0502-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/24/2017] [Indexed: 12/17/2022] Open
Abstract
Background Variability in drug efficacy and adverse effects are observed in clinical practice. While the extent of genetic variability in classic pharmacokinetic genes is rather well understood, the role of genetic variation in drug targets is typically less studied. Methods Based on 60,706 human exomes from the ExAC dataset, we performed an in-depth computational analysis of the prevalence of functional variants in 806 drug-related genes, including 628 known drug targets. We further computed the likelihood of 1236 FDA-approved drugs to be affected by functional variants in their targets in the whole ExAC population as well as different geographic sub-populations. Results We find that most genetic variants in drug-related genes are very rare (f < 0.1%) and thus will likely not be observed in clinical trials. Furthermore, we show that patient risk varies for many drugs and with respect to geographic ancestry. A focused analysis of oncological drug targets indicates that the probability of a patient carrying germline variants in oncological drug targets is, at 44%, high enough to suggest that not only somatic alterations but also germline variants carried over into the tumor genome could affect the response to antineoplastic agents. Conclusions This study indicates that even though many variants are very rare and thus likely not observed in clinical trials, four in five patients are likely to carry a variant with possibly functional effects in a target for commonly prescribed drugs. Such variants could potentially alter drug efficacy. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0502-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Charlotta Pauline Irmgard Schärfe
- Department of Systems Biology, Harvard Medical School, Boston, 02115, Massachusetts, USA.,Center for Bioinformatics, University of Tübingen, 72076, Tübingen, Germany.,pplied Bioinformatics, Department of Computer Science, 72076, Tübingen, Germany
| | - Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany.,Department of Clinical Pharmacology, University Hospital Tübingen, 72076, Tübingen, Germany.,Department of Pharmacy and Biochemistry, University of Tübingen, 72076, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, 72076, Tübingen, Germany. .,pplied Bioinformatics, Department of Computer Science, 72076, Tübingen, Germany. .,Quantitative Biology Center, 72076, Tübingen, Germany. .,Faculty of Medicine, University of Tübingen, 72076, Tübingen, Germany. .,Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
| | - Debora Susan Marks
- Department of Systems Biology, Harvard Medical School, Boston, 02115, Massachusetts, USA.
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Cell Cycle Model System for Advancing Cancer Biomarker Research. Sci Rep 2017; 7:17989. [PMID: 29269772 PMCID: PMC5740075 DOI: 10.1038/s41598-017-17845-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/27/2017] [Indexed: 01/14/2023] Open
Abstract
Progress in understanding the complexity of a devastating disease such as cancer has underscored the need for developing comprehensive panels of molecular markers for early disease detection and precision medicine applications. The present study was conducted to assess whether a cohesive biological context can be assigned to protein markers derived from public data mining, and whether mass spectrometry can be utilized to screen for the co-expression of functionally related biomarkers to be recommended for further exploration in clinical context. Cell cycle arrest/release experiments of MCF7/SKBR3 breast cancer and MCF10 non-tumorigenic cells were used as a surrogate to support the production of proteins relevant to aberrant cell proliferation. Information downloaded from the scientific public domain was queried with bioinformatics tools to generate an initial list of 1038 cancer-associated proteins. Mass spectrometric analysis of cell extracts identified 352 proteins that could be matched to the public list. Differential expression, enrichment, and protein-protein interaction analysis of the proteomic data revealed several functionally-related clusters of relevance to cancer. The results demonstrate that public data derived from independent experiments can be used to inform biological research and support the development of molecular assays for probing the characteristics of a disease.
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Johnson AA, Andrews-Pfannkoch C, Nelson TJ, Pulido JS, Marmorstein AD. Disease modeling studies using induced pluripotent stem cells: are we using enough controls? Regen Med 2017; 12:899-903. [PMID: 29243553 DOI: 10.2217/rme-2017-0101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The comparison of differentiated induced pluripotent stem cells (iPSCs) derived from patients with disease to differentiated iPSCs derived from healthy patients enables powerful disease modeling. By performing an informal retrospective survey of disease modeling studies published in high impact journals, we found that the median and average number of controls used in these studies were 1 and 1.6, respectively. The bulk of these studies did not control for age, gender and ethnicity. Since a large proportion of phenotypic differences observed between iPSC lines are due to genetic variation or variation between lines, this is an insufficient number of controls to confidently rule out standard variation. Future studies need to include more controls and ensure that these controls are appropriately matched for gender, age and ethnicity.
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Affiliation(s)
- Adiv A Johnson
- Department of Ophthalmology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Timothy J Nelson
- Departments of Cardiovascular Diseases, Molecular Pharmacology & Experimental Therapeutics, Division of General Internal Medicine, Division of Pediatric Cardiology, & Transplant Center, & Center for Regenerative Medicine, Rochester, MN 55905, USA
| | - Jose S Pulido
- Department of Ophthalmology, Mayo Clinic, Rochester, MN 55905, USA
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Heale BSE, Khalifa A, Stone BL, Nelson S, Del Fiol G. Physicians' pharmacogenomics information needs and seeking behavior: a study with case vignettes. BMC Med Inform Decis Mak 2017; 17:113. [PMID: 28764766 PMCID: PMC5540399 DOI: 10.1186/s12911-017-0510-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/19/2017] [Indexed: 11/10/2022] Open
Abstract
Background Genetic testing, especially in pharmacogenomics, can have a major impact on patient care. However, most physicians do not feel that they have sufficient knowledge to apply pharmacogenomics to patient care. Online information resources can help address this gap. We investigated physicians’ pharmacogenomics information needs and information-seeking behavior, in order to guide the design of pharmacogenomics information resources that effectively meet clinical information needs. Methods We performed a formative, mixed-method assessment of physicians’ information-seeking process in three pharmacogenomics case vignettes. Interactions of 6 physicians’ with online pharmacogenomics resources were recorded, transcribed, and analyzed for prominent themes. Quantitative data included information-seeking duration, page navigations, and number of searches entered. Results We found that participants searched an average of 8 min per case vignette, spent less than 30 s reviewing specific content, and rarely refined search terms. Participants’ information needs included a need for clinically meaningful descriptions of test interpretations, a molecular basis for the clinical effect of drug variation, information on the logistics of carrying out a genetic test (including questions related to cost, availability, test turn-around time, insurance coverage, and accessibility of expert support).Also, participants sought alternative therapies that would not require genetic testing. Conclusion This study of pharmacogenomics information-seeking behavior indicates that content to support their information needs is dispersed and hard to find. Our results reveal a set of themes that information resources can use to help physicians find and apply pharmacogenomics information to the care of their patients. Electronic supplementary material The online version of this article (doi:10.1186/s12911-017-0510-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bret S E Heale
- Department of Biomedical Informatics, University of Utah, 421 Wakara Way, Salt Lake City, UT, 84108, USA.,Intermountain Healthcare, West Valley, UT, USA
| | - Aly Khalifa
- Department of Biomedical Informatics, University of Utah, 421 Wakara Way, Salt Lake City, UT, 84108, USA
| | - Bryan L Stone
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Scott Nelson
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, 421 Wakara Way, Salt Lake City, UT, 84108, USA.
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Iyer PM, Karthikeyan S, Sanjay Kumar P, Krishnan Namboori PK. Comprehensive strategy for the design of precision drugs and identification of genetic signature behind proneness of the disease-a pharmacogenomic approach. Funct Integr Genomics 2017; 17:375-385. [PMID: 28470340 DOI: 10.1007/s10142-017-0559-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/05/2017] [Indexed: 12/20/2022]
Abstract
The proneness of diseases and susceptibility towards drugs vary from person to person. At present, there is a strong demand for the personalization of drugs. The genetic signature behind proneness of the disease has been studied through a comprehensive 'octopodial approach'. All the genetic variants included in the approach have been introduced. The breast cancer associated with BRCA1 mutation has been taken as the illustrative example to introduce all these factors. The genetic variants associated with the drug action of tamoxifen have been fully illustrated in the manuscript. The design of a new personalized anti-breast cancer drug has been explained in the third phase. For the design of new personalized drugs, a metabolite of anti-cancer drug chlorambucil has been taken as the template. The design of drug has been made with respect to the protein 1T15 of BRCA1 gene corresponding to the genetic signature of rs28897696.
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Affiliation(s)
- Preethi M Iyer
- Department of Electronics and Communication Engineering, M.Tech-Biomedical Engineering Amrita School of Engineering, AMRITA Vishwa Vidyapeetham Amrita University, Amritanagar, Ettimadai, Coimbatore, Tamil Nadu, 641112, India
| | - S Karthikeyan
- Amrita School of Engineering, AMRITA Vishwa Vidyapeetham Amrita University, Amritanagar, Ettimadai, Coimbatore, Tamil Nadu, 641112, India
| | - P Sanjay Kumar
- Amrita School of Engineering, AMRITA Vishwa Vidyapeetham Amrita University, Amritanagar, Ettimadai, Coimbatore, Tamil Nadu, 641112, India
| | - P K Krishnan Namboori
- Amrita School of Engineering, AMRITA Vishwa Vidyapeetham Amrita University, Amritanagar, Ettimadai, Coimbatore, Tamil Nadu, 641112, India.
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Brunetti A, Chiefari E, Foti DP. Pharmacogenetics in type 2 diabetes: still a conundrum in clinical practice. Expert Rev Endocrinol Metab 2017; 12:155-158. [PMID: 30063457 DOI: 10.1080/17446651.2017.1316192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Antonio Brunetti
- a Department of Health Sciences , University "Magna Græcia" of Catanzaro , Catanzaro , Italy
| | - Eusebio Chiefari
- a Department of Health Sciences , University "Magna Græcia" of Catanzaro , Catanzaro , Italy
| | - Daniela Patrizia Foti
- a Department of Health Sciences , University "Magna Græcia" of Catanzaro , Catanzaro , Italy
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Abstract
PURPOSE OF REVIEW To describe recent developments in the genetics of sporadic inclusion body myositis (sIBM). RECENT FINDINGS Genes located within major histocompatibility complex regions remain the strongest genetic association with sIBM. The rs10527454 polymorphism in the TOMM40 gene seems to have a disease modifying effect on sIBM by delaying the onset of symptoms, and this effect may be enhanced by the APOE ε3/ε3 genotype. Rare variants in the VCP and SQSTM1 genes have been identified in sIBM patients in two studies using targeted next-generation sequencing and whole-exome sequencing. Two studies have confirmed the correlation between the amount of cytochrome c oxidase -deficient fibres and the proportion of mitochondrial DNA (mtDNA) deletions in sIBM. Some rare variants in mtDNA-related nuclear genes have also been reported. SUMMARY There have been advances in the genetics of sIBM over the past 2 years facilitated by the use of next-generation sequencing. Genes that cause hereditary IBM, which has clinical or pathological features resembling sIBM, have provided clues to the genetic basis of sIBM. To date, genes located in major histocompatibility complex regions and genes involved in protein homeostasis or mtDNA maintenance have been implicated in sIBM. Whole-exome sequencing-association studies, RNA sequencing, and whole-genome sequencing in large sIBM cohorts will be key tools to unravel the genetics of sIBM and its contribution to disease aetiopathogenesis.
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Tien YC, Liu K, Pope C, Wang P, Ma X, Zhong XB. Dose of Phenobarbital and Age of Treatment at Early Life are Two Key Factors for the Persistent Induction of Cytochrome P450 Enzymes in Adult Mouse Liver. Drug Metab Dispos 2015; 43:1938-45. [PMID: 26400395 DOI: 10.1124/dmd.115.066316] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/21/2015] [Indexed: 02/01/2023] Open
Abstract
Drug treatment of neonates and infants and its long-term consequences on drug responses have emerged in recent years as a major challenge for health care professionals. In the current study, we use phenobarbital as a model drug and mouse as an in vivo model to demonstrate that the dose of phenobarbital and age of treatment are two key factors for the persistent induction of gene expression and consequential increases of enzyme activities of Cyp2b, Cyp2c, and Cyp3a in adult livers. We show that phenobarbital treatment at early life of day 5 after birth with a low dose (<100 mg/kg) does not change expression and enzyme activities of Cyp2b, Cyp2c, and Cyp3a in adult mouse liver, whereas phenobarbital treatment with a high dose (>200 mg/kg) significantly increases expression and enzyme activities of these P450s in adult liver. We also demonstrate that phenobarbital treatment before day 10 after birth, but not at later ages, significantly increases mRNAs, proteins, and enzyme activities of the tested P450s. Such persistent induction of P450 gene expression and enzyme activities in adult livers by phenobarbital treatment only occurs within a sensitive age window early in life. The persistent induction in gene expression and enzyme activities is higher in female mice than in male mice for Cyp2b10 but not for Cyp2c29 and Cyp3a11. These results will stimulate studies to evaluate the long-term impacts of drug treatment with different doses at neonatal and infant ages on drug metabolism, therapeutic efficacy, and drug-induced toxicity throughout the rest of life.
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Affiliation(s)
- Yun-Chen Tien
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.C.T., C.P., X.B.Z.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (K.L., P.W., X.M.)
| | - Ke Liu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.C.T., C.P., X.B.Z.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (K.L., P.W., X.M.)
| | - Chad Pope
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.C.T., C.P., X.B.Z.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (K.L., P.W., X.M.)
| | - Pengcheng Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.C.T., C.P., X.B.Z.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (K.L., P.W., X.M.)
| | - Xiaochao Ma
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.C.T., C.P., X.B.Z.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (K.L., P.W., X.M.)
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.C.T., C.P., X.B.Z.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (K.L., P.W., X.M.)
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Abstract
Formation of patterns is a common feature in the development of multicellular organism as well as of microbial communities. To investigate the formation of gene expression patterns in colonies, we build a mathematical model of two-dimensional colony growth, where cells carry a coupled positive-and-negative-feedback circuit. We demonstrate that the model can produce sectored, target (concentric), uniform, and scattered expression patterns of regulators, depending on gene expression dynamics and nutrient diffusion. We reconstructed the same regulatory structure in Escherichia coli cells and found gene expression patterns on the surface of colonies similar to the ones produced by the computer simulations. By comparing computer simulations and experimental results, we observed that very simple rules of gene expression can yield a spectrum of well-defined patterns in a growing colony. Our results suggest that variations of the protein content among cells lead to a high level of heterogeneity in colonies. Importance Formation of patterns is a common feature in the development of microbial communities. In this work, we show that a simple genetic circuit composed of a positive-feedback loop and a negative-feedback loop can produce diverse expression patterns in colonies. We obtained similar sets of gene expression patterns in the simulations and in the experiments. Because the combination of positive feedback and negative feedback is common in intracellular molecular networks, our results suggest that the protein content of cells is highly diversified in colonies. Formation of patterns is a common feature in the development of microbial communities. In this work, we show that a simple genetic circuit composed of a positive-feedback loop and a negative-feedback loop can produce diverse expression patterns in colonies. We obtained similar sets of gene expression patterns in the simulations and in the experiments. Because the combination of positive feedback and negative feedback is common in intracellular molecular networks, our results suggest that the protein content of cells is highly diversified in colonies.
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Cree SL, Kennedy MA. Relevance of G-quadruplex structures to pharmacogenetics. Front Pharmacol 2014; 5:160. [PMID: 25071578 PMCID: PMC4085647 DOI: 10.3389/fphar.2014.00160] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/19/2014] [Indexed: 12/21/2022] Open
Abstract
G-quadruplexes are non-canonical secondary structures formed within nucleic acids that are involved in modulating cellular processes such as replication, gene regulation, recombination and epigenetics. Within genes, there is mounting evidence of G-quadruplex involvement in transcriptional and post transcriptional regulation. We report the presence of potential G-quadruplex motifs within relevant sites of some important pharmacogenes and discuss the possible implications of this on the function and expression of these genes. Appreciating the location and potential functions of these motifs may be of value when considering the impacts of some pharmacogenetic variants. G-quadruplexes are also the focus of drug development efforts in oncology and we highlight the broader pharmacological implications of treatment strategies that may target G-quadruplexes.
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Affiliation(s)
- Simone L Cree
- Department of Pathology, Carney Centre for Pharmacogenomics, University of Otago Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology, Carney Centre for Pharmacogenomics, University of Otago Christchurch, New Zealand
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Pirmohamed M. Personalized pharmacogenomics: predicting efficacy and adverse drug reactions. Annu Rev Genomics Hum Genet 2014; 15:349-70. [PMID: 24898040 DOI: 10.1146/annurev-genom-090413-025419] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Drug response varies between individuals owing to disease heterogeneity, environmental factors, and genetic factors. Genetic factors can affect both the pharmacokinetics and pharmacodynamics of a drug, leading to changes in local and systemic drug exposure and/or changes in the function of the drug target, altering drug response. Several pharmacogenetic biomarkers are already utilized in clinical practice and have been shown to improve clinical outcomes. However, a large number of other biomarkers have never made it beyond the discovery stage. Concerted effort is needed to improve the translation of pharmacogenetic biomarkers into clinical practice, and this will involve the use of standardized phenotyping and genotyping strategies, collaborative work, multidisciplinary approaches to identifying and replicating associations, and cooperation with industry to facilitate translation and commercialization. Acceptance of these approaches by clinicians, regulators, patients, and the public will be important in determining future success.
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Affiliation(s)
- Munir Pirmohamed
- Wolfson Centre for Personalised Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GL, United Kingdom;
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Nishino J, Sugiyama M, Nishida N, Tokunaga K, Mizokami M, Mano S. The interaction of a single-nucleotide polymorphism with age on response to interferon-α and ribavirin therapy in female patients with hepatitis C infection. J Med Virol 2014; 86:1130-3. [PMID: 24692042 DOI: 10.1002/jmv.23939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2014] [Indexed: 11/08/2022]
Abstract
Older female patients exhibit a poor response to the current standard treatment for hepatitis C, interferon-α, and ribavirin (PEG-IFN-α/RBV). In this study, we reported that the combination of age and the genotype of a novel SNP can predict response to standard treatment (P = 7.31 × 10(-8)). The model incorporating genotype of the novel SNP, rs1287948, predicts response more accurately (AUC = 0.934; 95% CI = 0.881-0.988) in women as compared with the model using age and the previously identified SNP, rs8099917.
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Affiliation(s)
- Jo Nishino
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
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Drögemöller BI, Wright GEB, Warnich L. Considerations for rare variants in drug metabolism genes and the clinical implications. Expert Opin Drug Metab Toxicol 2014; 10:873-84. [PMID: 24673405 DOI: 10.1517/17425255.2014.903239] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Large-scale whole genome and exome resequencing studies have revealed that humans have a high level of deleterious rare variation, which has important implications for the design of future pharmacogenetics studies. AREAS COVERED Current pharmacogenetic guidelines focus on the implementation of common variation into dosing guidelines. However, it is becoming apparent that rare variation may also play an important role in differential drug response. Current sequencing technologies offer the opportunity to examine rare variation, but there are many challenges associated with such analyses. Nonetheless, if a comprehensive picture of the role that genetic variants play in treatment outcomes is to be obtained, it will be necessary to include the entire spectrum of variation, including rare variants, into pharmacogenetic research. EXPERT OPINION In order to implement pharmacogenetics in the clinic, patients should be genotyped for clinically actionable pharmacogenetic variants and patients responding unfavourably to treatment after pharmacogenetics-based dosing should be identified and resequenced to identify additional functionally relevant variants, including rare variants. All derived information should be added to a central database to allow for the updating of existing dosing guidelines. By routinely implementing such strategies, pharmacogenetics-based treatment guidelines will continue to improve.
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Tang Y. A one-step imaging assay to monitor cell cycle state and apoptosis in mammalian cells. ACTA ACUST UNITED AC 2014; 6:1-5. [PMID: 24652619 DOI: 10.1002/9780470559277.ch130140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
High-content screening (HCS; fluorescence microscopy with multiple markers followed by automated image analysis) is gaining popularity in drug discovery due to the rich information it reveals about drug responses. It is particularly useful in studying anti-mitotic drug responses since mitotic arrest provides an activity biomarker. One conventional way to probe mitotic arrest and downstream apoptosis response is to use mitosis- and apoptosis-specific antibodies in cell-based imaging assays. However, weakly attached cells, especially dead cells, are mostly washed out during antibody labeling steps. Here, we report a rapid and convenient one-step cell-imaging assay that accurately measures cell-cycle state and apoptosis in mammalian cells. The assay uses three fluorescent dyes to stain living cells, involves no wash, and is fixable after live-cell labeling. Compared to the antibody-based method, this assay is quicker, more cost-effective, and yields more accurate dose-response results.
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Affiliation(s)
- Yangzhong Tang
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.,Sanofi, Cambridge, Massachusetts
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