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Lewandrowski KU, Sharafshah A, Elfar J, Schmidt SL, Blum K, Wetzel FT. A Pharmacogenomics-Based In Silico Investigation of Opioid Prescribing in Post-operative Spine Pain Management and Personalized Therapy. Cell Mol Neurobiol 2024; 44:47. [PMID: 38801645 PMCID: PMC11129978 DOI: 10.1007/s10571-024-01466-5] [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: 12/07/2023] [Accepted: 02/26/2024] [Indexed: 05/29/2024]
Abstract
Considering the variability in individual responses to opioids and the growing concerns about opioid addiction, prescribing opioids for postoperative pain management after spine surgery presents significant challenges. Therefore, this study undertook a novel pharmacogenomics-based in silico investigation of FDA-approved opioid medications. The DrugBank database was employed to identify all FDA-approved opioids. Subsequently, the PharmGKB database was utilized to filter through all variant annotations associated with the relevant genes. In addition, the dpSNP ( https://www.ncbi.nlm.nih.gov/snp/ ), a publicly accessible repository, was used. Additional analyses were conducted using STRING-MODEL (version 12), Cytoscape (version 3.10.1), miRTargetLink.2, and NetworkAnalyst (version 3). The study identified 125 target genes of FDA-approved opioids, encompassing 7019 variant annotations. Of these, 3088 annotations were significant and pertained to 78 genes. During variant annotation assessments (VAA), 672 variants remained after filtration. Further in-depth filtration based on variant functions yielded 302 final filtered variants across 56 genes. The Monoamine GPCRs pathway emerged as the most significant signaling pathway. Protein-protein interaction (PPI) analysis revealed a fully connected network comprising 55 genes. Gene-miRNA Interaction (GMI) analysis of these 55 candidate genes identified miR-16-5p as a pivotal miRNA in this network. Protein-Drug Interaction (PDI) assessment showed that multiple drugs, including Ibuprofen, Nicotine, Tramadol, Haloperidol, Ketamine, L-Glutamic Acid, Caffeine, Citalopram, and Naloxone, had more than one interaction. Furthermore, Protein-Chemical Interaction (PCI) analysis highlighted that ABCB1, BCL2, CYP1A2, KCNH2, PTGS2, and DRD2 were key targets of the proposed chemicals. Notably, 10 chemicals, including carbamylhydrazine, tetrahydropalmatine, Terazosin, beta-methylcholine, rubimaillin, and quinelorane, demonstrated dual interactions with the aforementioned target genes. This comprehensive review offers multiple strong, evidence-based in silico findings regarding opioid prescribing in spine pain management, introducing 55 potential genes. The insights from this report can be applied in exome analysis as a pharmacogenomics (PGx) panel for pain susceptibility, facilitating individualized opioid prescribing through genotyping of related variants. The article also points out that African Americans represent an important group that displays a high catabolism of opioids and suggest the need for a personalized therapeutic approach based on genetic information.
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Affiliation(s)
- Kai-Uwe Lewandrowski
- Division of Personalized Pain Therapy Research & Education, Center for Advanced Spine Care of Southern Arizona, Arizona, USA.
- Department of Orthopaedics, Fundación Universitaria Sanitas and Member of Colombian National Academy of Medicine, Bogotá, DC, Colombia.
- Department of Orthopedics, Doctor honoris causa Hospital Universitário Gaffree Guinle Universidade Federal do Estado do Rio de Janeiro, and Member of the Brazilian National Academy of Medicine, Rio de Janeiro, Brazil.
- Center for Advanced Spine Care of Southern Arizona, 4787 E Camp Lowell Drive, Tucson, USA.
| | - Alireza Sharafshah
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - John Elfar
- Department of Orthopaedics and Sports Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Sergio Luis Schmidt
- Department of Neurology, Federal University of Rio de Janeiro (UNIRIO), University Hospital, Rua Mariz e Barros 750, Tijuca, Rio de Janeiro, RJ, Brazil
| | - Kenneth Blum
- Division of Nutrigenomics, SpliceGen, Therapeutics, Inc., Austin, TX, 78701, USA
- Department of Psychiatry, Wright State University Boonshoft School of Medicine, Dayton, OH, 45435, USA
- Division of Addiction Research & Education, Center for Sports, Exercise, & Mental Health, Western University Health Sciences, Pomona, CA, 91766, USA
- The Kenneth Blum Behavioral & Neurogenetic Institute, LLC., Austin, TX, 78701, USA
| | - Franklin Todd Wetzel
- Department of Orthopaedic Surgery & Sports Medicine, Director of Musculoskeletal Services Bassett Healthcare Network 1 Atwell Road, Cooperstown, NY, 13326, USA
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Liu Q, Wang F, Wang G, Liu L, Hu X. Recent evidence and progress for developing precision nursing in symptomatology: A scoping review. Int Nurs Rev 2023; 70:415-424. [PMID: 36597558 DOI: 10.1111/inr.12816] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/24/2022] [Indexed: 01/05/2023]
Abstract
AIM To summarize the omics results of symptomatic research that can help nurses identify intervention targets and design precision interventions for pain, mental health, cognitive impairment, sleep disorder, fatigue, lymphedema, and quality of life, so as to provide a comprehensive summary of help and inspire to precision nursing. METHODS CINAHL, PubMed, Web of Science, and ScienceDirect databases were searched. Retrieval time was from January 2012 to December 2021. Symptomatology research applying omics that can be used to guide nurses in designing targeted interventions was included. RESULTS Forty-six studies were included in the final review. Symptomatology research that can be integrated with nursing science to develop precision nursing focused on pain, mental health, cognitive impairment, sleep disorder, fatigue, lymphedema, and quality of life. Most studies were related to cognitive impairment (n = 10; 21.74%), pain (n = 9; 19.57%), and mental health (n = 8; 17.39%). Moreover, the included studies involved various omics technologies, such as whole genome, epigenome, transcriptome, proteome, and metabolome. CONCLUSION The rapid development of various omic technologies promotes symptomatology research, which can help nurses fully understand the information of patients. Phenotypic characteristics and biomarkers shown in symptomatology research help nurses identify intervention targets and develop individualization interventions, so as to prevent and reduce symptoms and improve the quality of life. IMPLICATION FOR NURSING AND HEALTH POLICY This scoping review is the first synthesis of all peer-reviewed literature to summarize and provide important information and references from the omic results of symptomatology studies to develop precision nursing, highlighting the status and development of precision nursing. Nursing education policies should introduce the development and importance of precision nursing. Further research could consider investing more attention in precision nursing. Nursing researchers can carry out some studies applying omics technology to explore more biomarkers, helping guide the formulation of clinical intervention for symptoms.
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Affiliation(s)
- Qian Liu
- West China School of Nursing, Sichuan University/ Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Sichuan, China
| | - Fang Wang
- West China School of Nursing, Sichuan University/ Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Sichuan, China
| | - Guan Wang
- West China School of Nursing, Sichuan University/ Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Sichuan, China
| | - Li Liu
- West China School of Nursing, Sichuan University/ Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Sichuan, China
| | - Xiuying Hu
- West China School of Nursing, Sichuan University/ Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Sichuan, China
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3
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蒋 慧, 熊 代, 张 瑞. [Application Status and Prospects of Precision Nursing Under the Concept of Enhanced Recovery After Surgery]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:712-716. [PMID: 37545061 PMCID: PMC10442622 DOI: 10.12182/20230760503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 08/08/2023]
Abstract
With the development of enhanced recovery after surgery (ERAS), major breakthroughs have been made in this field of study. However, the research fields still need to be continuously expanded to meet the needs of patients. The concept of precision therapy is widely applied in the field of nursing. Under the concept of ERAS, practical studies of applying precision nursing for the perioperative period have already been conducted, exploring such issues as precision nursing assessment, precision nursing intervention design, precision risk prediction model, and information technology to assist precision nursing practice. Research findings have preliminarily validated the safety and effectiveness of applying precision nursing for ERAS in the perioperative period. Herein, we reviewed the reported findings of relevant research published in recent years and identified the following problems in the implementation of precision nursing under the ERAS concept, a lack of implementation standards, challenges concerning the the role of nurses, a lack of high-quality research evidence in the existing literature, and a relevant big data processing platform that China does not have and therefore cannot carry out data sharing, integration, mining, and utilization. We also made suggestions for effective improvement and discussed research prospects. In the future, multidisciplinary collaboration, translational medical research, and the development of various innovative tools are to be strengthened to help improve the quality and effectiveness of nursing care. We hope to provide reference for improving the scientific and targeted implementation of precision nursing for ERAS in the perioperative period.
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Affiliation(s)
- 慧琴 蒋
- 广东省人民医院(广东省医学科学院) (广州 510080)Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, China
| | - 代兰 熊
- 广东省人民医院(广东省医学科学院) (广州 510080)Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, China
| | - 瑞英 张
- 广东省人民医院(广东省医学科学院) (广州 510080)Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, China
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4
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Ateia H, Ogrodzki P, Wilson HV, Ganesan S, Halwani R, Koshy A, Zaher WA. Population Genome Programs across the Middle East and North Africa: Successes, Challenges, and Future Directions. Biomed Hub 2023; 8:60-71. [PMID: 37900972 PMCID: PMC10601860 DOI: 10.1159/000530619] [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: 09/23/2022] [Accepted: 03/29/2023] [Indexed: 10/31/2023] Open
Abstract
In this review, we discuss the current state of population genome programs (PGPs) conducted in the Middle East and North African (MENA) region. This region has high prevalence of genetic diseases and significant health challenges as well as being a significantly underrepresented population in public genetic databases. The majority of ongoing PGPs represent regions in Europe, North and South America, South Asia, Australia, and Africa, with little to no descriptive information highlighted only on the MENA Region when it comes to genome programs databases, outcomes, or the challenges that MENA region countries may face establishing their own national programs. This review has identified 6 PGPs currently underway in the MENA region, namely in the Kingdom of Saudi Arabia, Qatar, Egypt, the United Arab Emirates, Bahrain, and Iran. Due to the rapidly growing involvement of the MENA region in national-scale genomic data collection, an increase in representation in public genetic databases is to be expected to occur in the near future. Whilst significant progress is being made in some MENA countries, future initiatives as well as ongoing programs will be facing several challenges related to collaboration, finance, infrastructure and institutional data access, data analysis, sustainability, health records, and biobanks. The review also reiterates the need for ensuring ethical and regulated genomic initiatives which can drive developments in personalized medicine treatments to improve patient prognosis and quality of life.
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Affiliation(s)
- Hagar Ateia
- G42 Healthcare, Masdar City Abu Dhabi, UAE
- IROS (Insights Research Organization and Solutions), Abu Dhabi, UAE
| | | | - Hannah V. Wilson
- IROS (Insights Research Organization and Solutions), Abu Dhabi, UAE
| | - Subhashini Ganesan
- G42 Healthcare, Masdar City Abu Dhabi, UAE
- IROS (Insights Research Organization and Solutions), Abu Dhabi, UAE
| | | | | | - Walid A. Zaher
- G42 Healthcare, Masdar City Abu Dhabi, UAE
- IROS (Insights Research Organization and Solutions), Abu Dhabi, UAE
- UAE University, Al Ain, UAE
- Khalifa University, Abu Dhabi, UAE
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5
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Tromans E, Barwell J. Clinical genetics: past, present and future. Eur J Hum Genet 2022; 30:991-992. [PMID: 35075300 PMCID: PMC9437011 DOI: 10.1038/s41431-022-01041-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/19/2021] [Accepted: 01/07/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Eva Tromans
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, LE1 5WW, UK.
| | - Julian Barwell
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, LE1 5WW, UK.,Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7 RH, UK
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6
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Donohue KE, Dolan SM, Watnick D, Gallagher KM, Odgis JA, Suckiel SA, Teitelman N, Gelb BD, Kenny EE, Wasserstein MP, Horowitz CR, Bauman LJ. Hope versus reality: Parent expectations of genomic testing. PATIENT EDUCATION AND COUNSELING 2021; 104:2073-2079. [PMID: 33640235 PMCID: PMC8679507 DOI: 10.1016/j.pec.2021.01.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 05/11/2023]
Abstract
OBJECTIVE Genomics is increasingly used for diagnostic testing in children. This study describes the expectations of parents whose child received genomic testing and whether or not they were met. METHODS A diverse stratified, purposive sample of parents of 22 children in New York City was interviewed using a semi-structured guide. Genomic test results were positive, negative, or uncertain. RESULTS Parents expressed their expectations in narrative and numeric fashion. Parents expected that their child's test would have a direct effect on their child's diagnosis. Some believed that results would be definitive, while others recognized testing limitations. Expectations reflected parents' hope to find a diagnosis and led to disappointment when results were uninformative or did not impact clinical management. CONCLUSION Results suggest pre-test genetic counseling emphasize the low likelihood of actionable results; however, parents' expectations of genomics' diagnostic capabilities are strongly rooted in their need to end the diagnostic odyssey and may be difficult to manage. PRACTICE IMPLICATIONS Parents' hope for a resolution and effective treatment for their child is a powerful context in which genetic counseling is heard. Clinicians who provide genomic testing should continue to acknowledge parents' preconceptions. Additional research in other settings will help understand how to best address and manage parent expectations of genomic medicine.
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Affiliation(s)
- Katherine E Donohue
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Siobhan M Dolan
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Dana Watnick
- Department of Pediatrics, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States
| | - Katie M Gallagher
- Department of Pediatrics, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States
| | - Jacqueline A Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sabrina A Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nehama Teitelman
- Department of Pediatrics, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Melissa P Wasserstein
- Department of Pediatrics, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States
| | - Carol R Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Laurie J Bauman
- Department of Pediatrics, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States; Department of Psychiatry and Behavioral Sciences, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States.
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7
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García-Foncillas J, Argente J, Bujanda L, Cardona V, Casanova B, Fernández-Montes A, Horcajadas JA, Iñiguez A, Ortiz A, Pablos JL, Pérez Gómez MV. Milestones of Precision Medicine: An Innovative, Multidisciplinary Overview. Mol Diagn Ther 2021; 25:563-576. [PMID: 34331269 DOI: 10.1007/s40291-021-00544-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2021] [Indexed: 12/11/2022]
Abstract
Although the concept of precision medicine, in which healthcare is tailored to the molecular and clinical characteristics of each individual, is not new, its implementation in clinical practice has been heterogenous. In some medical specialties, precision medicine has gone from being just a promise to a reality that achieves better patient outcomes. This is a fact if we consider, for example, the great advances made in the genetic diagnosis and subsequent treatment of countless hereditary diseases, such as cystic fibrosis, which have improved the life expectancy of many of the affected children. In the field of oncology, the development of targeted therapies has prolonged the survival of patients with breast, lung, colorectal, melanoma, and hematological malignancies. In other disciplines, clinical milestones are perhaps less well known, but no less important. The current challenge is to expand and generalize the use of technologies that are central to precision medicine, such as massively parallel sequencing, to improve the management (prevention and treatment) of complex conditions such as cardiovascular, kidney, or autoimmune diseases. This process requires investment in specialized expertise, multidisciplinary collaboration, and the nationwide organization of genetic laboratories for diagnosis of specific diseases.
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Affiliation(s)
- Jesús García-Foncillas
- Department of Oncology, Oncohealth Institute, Fundacion Jimenez Diaz University Hospital, Autonomous University, Madrid, Spain. .,Medical Oncology Department, University Hospital Fundación Jiménez Díaz-Universidad Autonoma de Madrid, Madrid, Spain.
| | - Jesús Argente
- Department of Endocrinology, Instituto de Salud Carlos III, IMDEA Institute, Hospital Infantil Universitario Niño Jesús, Spanish PUBERE Registry, CIBER of Obesity and Nutrition (CIBEROBN), Universidad Autónoma de Madrid, Madrid, Spain.,Department of Pediatrics, Instituto de Salud Carlos III, IMDEA Institute, Hospital Infantil Universitario Niño Jesús, Spanish PUBERE Registry, CIBER of Obesity and Nutrition (CIBEROBN), Universidad Autónoma de Madrid, Madrid, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universidad del País Vasco (UPV/EHU), San Sebastian, Spain
| | - Victoria Cardona
- Allergy Section, Department of Internal Medicine, Hospital Vall d'Hebron, Barcelona, Spain.,ARADyAL Research Network, Barcelona, Spain
| | - Bonaventura Casanova
- Neuroimmunology Unit, La Fe University and Polytechnic Hospital, Valencia, Spain.,Department of Medicine, Faculty of Medicine, University of Valencia, Valencia, Spain
| | - Ana Fernández-Montes
- Medical Oncology, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | | | - Andrés Iñiguez
- Department of Cardiology, Hospital Álvaro Cunqueiro-Complejo Hospitalario Universitario, Vigo, Spain
| | - Alberto Ortiz
- Department of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz-UAM, Madrid, Spain
| | - José L Pablos
- Grupo de Enfermedades Inflamatorias y Autoinmunes, Instituto de Investigación Hospital 12 de Octubre, Madrid, Spain.,Servicio de Reumatología, Hospital 12 de Octubre, Universidad Complutense de Madrid, Madrid, Spain
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8
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Bi W, Lee S. Scalable and Robust Regression Methods for Phenome-Wide Association Analysis on Large-Scale Biobank Data. Front Genet 2021; 12:682638. [PMID: 34211504 PMCID: PMC8239389 DOI: 10.3389/fgene.2021.682638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
With the advances in genotyping technologies and electronic health records (EHRs), large biobanks have been great resources to identify novel genetic associations and gene-environment interactions on a genome-wide and even a phenome-wide scale. To date, several phenome-wide association studies (PheWAS) have been performed on biobank data, which provides comprehensive insights into many aspects of human genetics and biology. Although inspiring, PheWAS on large-scale biobank data encounters new challenges including computational burden, unbalanced phenotypic distribution, and genetic relationship. In this paper, we first discuss these new challenges and their potential impact on data analysis. Then, we summarize approaches that are scalable and robust in GWAS and PheWAS. This review can serve as a practical guide for geneticists, epidemiologists, and other medical researchers to identify genetic variations associated with health-related phenotypes in large-scale biobank data analysis. Meanwhile, it can also help statisticians to gain a comprehensive and up-to-date understanding of the current technical tool development.
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Affiliation(s)
- Wenjian Bi
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, United States
| | - Seunggeun Lee
- Graduate School of Data Science, Seoul National University, Seoul, South Korea
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9
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Piñero J, Saüch J, Sanz F, Furlong LI. The DisGeNET cytoscape app: Exploring and visualizing disease genomics data. Comput Struct Biotechnol J 2021; 19:2960-2967. [PMID: 34136095 PMCID: PMC8163863 DOI: 10.1016/j.csbj.2021.05.015] [Citation(s) in RCA: 226] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 02/07/2023] Open
Abstract
Thanks to the unbiased exploration of genomic variants at large scale, hundreds of thousands of disease-associated loci have been uncovered. In parallel, network-based approaches have proven to be essential to understand the molecular mechanisms underlying human diseases. The use of these approaches has been boosted by the abundance of information about disease associated genes and variants, high quality human interactomics data, and the emergence of new types of omics data. The DisGeNET Cytoscape App combines the capabilities of Cytoscape with those of DisGeNET, a knowledge platform based on a comprehensive catalogue of disease-associated genes and variants. The DisGeNET Cytoscape App contains functions to query, analyze, and visualize different network representations of the gene-disease and variant-disease associations available in DisGeNET. It supports a wide variety of applications through its query and filter functionalities, including the annotation of foreign networks generated by other apps or uploaded by the user. The new release of the DisGeNET Cytoscape App has been designed to support Cytoscape 3.x and incorporates novel distinctive features such as visualization and analysis of variant-disease networks, disease enrichment analysis for genes and variants, and analytic support through Cytoscape Automation. Moreover, the DisGeNET Cytoscape App features an API to access its core functionalities via the REST protocol fostering the development of reproducible and scalable analysis workflows based on DisGeNET data.
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Affiliation(s)
- Janet Piñero
- Research Group on Integrative Biomedical Informatics (GRIB), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- MedBioinformatics Solutions SL, Barcelona, Spain
| | - Josep Saüch
- Research Group on Integrative Biomedical Informatics (GRIB), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ferran Sanz
- Research Group on Integrative Biomedical Informatics (GRIB), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- MedBioinformatics Solutions SL, Barcelona, Spain
| | - Laura I. Furlong
- Research Group on Integrative Biomedical Informatics (GRIB), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- MedBioinformatics Solutions SL, Barcelona, Spain
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10
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Kovanda A, Zimani AN, Peterlin B. How to design a national genomic project-a systematic review of active projects. Hum Genomics 2021; 15:20. [PMID: 33761998 PMCID: PMC7988644 DOI: 10.1186/s40246-021-00315-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/23/2021] [Indexed: 01/18/2023] Open
Abstract
An increasing number of countries are investing efforts to exploit the human genome, in order to improve genetic diagnostics and to pave the way for the integration of precision medicine into health systems. The expected benefits include improved understanding of normal and pathological genomic variation, shorter time-to-diagnosis, cost-effective diagnostics, targeted prevention and treatment, and research advances.We review the 41 currently active individual national projects concerning their aims and scope, the number and age structure of included subjects, funding, data sharing goals and methods, and linkage with biobanks, medical data, and non-medical data (exposome). The main aims of ongoing projects were to determine normal genomic variation (90%), determine pathological genomic variation (rare disease, complex diseases, cancer, etc.) (71%), improve infrastructure (59%), and enable personalized medicine (37%). Numbers of subjects to be sequenced ranges substantially, from a hundred to over a million, representing in some cases a significant portion of the population. Approximately half of the projects report public funding, with the rest having various mixed or private funding arrangements. 90% of projects report data sharing (public, academic, and/or commercial with various levels of access) and plan on linking genomic data and medical data (78%), existing biobanks (44%), and/or non-medical data (24%) as the basis for enabling personal/precision medicine in the future.Our results show substantial diversity in the analysed categories of 41 ongoing national projects. The overview of current designs will hopefully inform national initiatives in designing new genomic projects and contribute to standardisation and international collaboration.
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Affiliation(s)
- Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia
| | - Ana Nyasha Zimani
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia.
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11
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Zhong M, van der Walt A, Campagna MP, Stankovich J, Butzkueven H, Jokubaitis V. The Pharmacogenetics of Rituximab: Potential Implications for Anti-CD20 Therapies in Multiple Sclerosis. Neurotherapeutics 2020; 17:1768-1784. [PMID: 33058021 PMCID: PMC7851267 DOI: 10.1007/s13311-020-00950-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
There are a broad range of disease-modifying therapies (DMTs) available in relapsing-remitting multiple sclerosis (RRMS), but limited biomarkers exist to personalise DMT choice. All DMTs, including monoclonal antibodies such as rituximab and ocrelizumab, are effective in preventing relapses and preserving neurological function in MS. However, each agent harbours its own risk of therapeutic failure or adverse events. Pharmacogenetics, the study of the effects of genetic variation on therapeutic response or adverse events, could improve the precision of DMT selection. Pharmacogenetic studies of rituximab in MS patients are lacking, but pharmacogenetic markers in other rituximab-treated autoimmune conditions have been identified. This review will outline the wider implications of pharmacogenetics and the mechanisms of anti-CD20 agents in MS. We explore the non-MS rituximab literature to characterise pharmacogenetic variants that could be of prognostic relevance in those receiving rituximab, ocrelizumab or other monoclonal antibodies for MS.
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Affiliation(s)
- Michael Zhong
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia.
- Department of Neurology, Alfred Health, Level 6, Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia.
| | - Anneke van der Walt
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Level 6, Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia
| | - Maria Pia Campagna
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Jim Stankovich
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Helmut Butzkueven
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Level 6, Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia
| | - Vilija Jokubaitis
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Level 6, Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia
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12
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Mochida K, Nishii R, Hirayama T. Decoding Plant-Environment Interactions That Influence Crop Agronomic Traits. PLANT & CELL PHYSIOLOGY 2020; 61:1408-1418. [PMID: 32392328 PMCID: PMC7434589 DOI: 10.1093/pcp/pcaa064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/26/2020] [Indexed: 05/16/2023]
Abstract
To ensure food security in the face of increasing global demand due to population growth and progressive urbanization, it will be crucial to integrate emerging technologies in multiple disciplines to accelerate overall throughput of gene discovery and crop breeding. Plant agronomic traits often appear during the plants' later growth stages due to the cumulative effects of their lifetime interactions with the environment. Therefore, decoding plant-environment interactions by elucidating plants' temporal physiological responses to environmental changes throughout their lifespans will facilitate the identification of genetic and environmental factors, timing and pathways that influence complex end-point agronomic traits, such as yield. Here, we discuss the expected role of the life-course approach to monitoring plant and crop health status in improving crop productivity by enhancing the understanding of plant-environment interactions. We review recent advances in analytical technologies for monitoring health status in plants based on multi-omics analyses and strategies for integrating heterogeneous datasets from multiple omics areas to identify informative factors associated with traits of interest. In addition, we showcase emerging phenomics techniques that enable the noninvasive and continuous monitoring of plant growth by various means, including three-dimensional phenotyping, plant root phenotyping, implantable/injectable sensors and affordable phenotyping devices. Finally, we present an integrated review of analytical technologies and applications for monitoring plant growth, developed across disciplines, such as plant science, data science and sensors and Internet-of-things technologies, to improve plant productivity.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- Corresponding author: E-mail, ; Fax, +81-45-503-9609
| | - Ryuei Nishii
- School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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13
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Bancroft EK, Kohut K, Eeles RA. The New Genomics Era: Integration of genomics into mainstream oncology and implications for psycho-oncological care. Psychooncology 2020; 29:453-460. [PMID: 32017261 DOI: 10.1002/pon.5331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Elizabeth K Bancroft
- Royal Marsden NHS Foundation Trust, London, UK.,The Institute of Cancer Research, London, UK
| | | | - Rosalind A Eeles
- Royal Marsden NHS Foundation Trust, London, UK.,The Institute of Cancer Research, London, UK
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