51
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Genetic profiling for disease stratification in chronic obstructive pulmonary disease and asthma. Curr Opin Pulm Med 2020; 25:317-322. [PMID: 30762612 DOI: 10.1097/mcp.0000000000000568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW In asthma and chronic obstructive pulmonary disease (COPD), the movement towards genetic profiling with a push towards 'personalized medicine' has been hindered by complex environment--gene interactions and lack of tools to identify clear causal genetic traits. In this review, we will discuss the need for genetic profiling in asthma and COPD, what methods are currently used in the clinics and the recent finding using new sequencing methods. RECENT FINDINGS Over the past 10-15 years, genome-wide association studies analysis of common variants has provide little in the way of new genetic profiling markers for asthma and COPD. Whole exome/genome sequencing has provided a new method to identify lowly abundant alleles, which might have a much higher impact. Although, low population numbers due to high costs has hindered early studies, recent studies have reached genome wide significance. SUMMARY The use of genetic profiling of COPD in the clinic is current limited to the identification of Alpha-1 antitrypsin deficiency, while being absent in asthma. Advances in sequencing technology provide new avenues to identify disease causes or therapy response altering variants that in the short-term will allow for the development of screening procedures for disease to identify patients at risk of developing asthma or COPD.
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52
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Lack S, Kinser PA. The modification of three vulnerability theories to assist nursing practice for school-age children with severe asthma. J SPEC PEDIATR NURS 2020; 25:e12280. [PMID: 31749322 DOI: 10.1111/jspn.12280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/01/2019] [Accepted: 11/06/2019] [Indexed: 11/27/2022]
Abstract
PURPOSE Severe asthma is an inflammatory illness associated with adverse health outcomes and behaviors in children, such as decreased quality of life, impaired sleep, and increased medical costs and morbidity. CONCLUSIONS Children with severe asthma frequently exhibit a cycle of health and behaviors which contribute to these adverse health outcomes, consisting of decreased physical activity, increased stress, and increased airway inflammation and asthma exacerbations. School-age children, in particular, are a vulnerable population because they not only rely on others for their care but also suffer from a chronic illness and are at risk for unequal healthcare access and health outcomes. PRACTICE IMPLICATIONS Currently, there is no one nursing theory that adequately addresses the vulnerability, cycle of health and behaviors, and adverse health outcomes of children with severe asthma. By integrating key concepts from three vulnerability theories and presenting a modified conceptual framework, this paper aims to demonstrate how the use of this new conceptual framework may assist nurses in evaluating the unique needs of school-age children with severe asthma to provide best practices and develop appropriate interventions.
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Affiliation(s)
- Sharon Lack
- School of Nursing, Virginia Commonwealth University, Richmond, Virginia
| | - Patricia A Kinser
- School of Nursing, Virginia Commonwealth University, Richmond, Virginia
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53
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Perez-Garcia J, Espuela-Ortiz A, Lorenzo-Diaz F, Pino-Yanes M. Pharmacogenetics of Pediatric Asthma: Current Perspectives. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2020; 13:89-103. [PMID: 32256100 PMCID: PMC7090194 DOI: 10.2147/pgpm.s201276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/03/2020] [Indexed: 12/11/2022]
Abstract
Asthma is a chronic respiratory disease that affects 339 million people worldwide and has a considerable impact on the pediatric population. Asthma symptoms can be controlled by pharmacological treatment. However, some patients do not respond to therapy and continue suffering from symptoms, which impair the quality of life of patients and limit their daily activity. Genetic variation has been shown to have a role in treatment response. The aim of this review is to update the main findings described in pharmacogenetic studies of pediatric asthma published from January 1, 2018 to December 31, 2019. During this period, the response to short-acting beta-agonists and inhaled corticosteroids in childhood asthma has been evaluated by eleven candidate-gene studies, one meta-analysis of a candidate gene, and six pharmacogenomic studies. The findings have allowed validating the association of genes previously related to asthma treatment response (ADRB2, GSDMB, FCER2, VEGFA, SPAT2SL, ASB3, and COL2A1), and identifying novel associations (PRKG1, DNAH5, IL1RL1, CRISPLD2, MMP9, APOBEC3B-APOBEC3C, EDDM3B, and BBS9). However, some results are not consistent across studies, highlighting the need to conduct larger studies in diverse populations with more homogeneous definitions of treatment response. Once stronger evidence was established, genetic variants will have the potential to be applied in clinical practice as biomarkers of treatment response enhancing asthma management and improving the quality of life of asthma patients.
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Affiliation(s)
- Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Antonio Espuela-Ortiz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Fabian Lorenzo-Diaz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain.,Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Comunidad de Madrid, Spain.,Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
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Abstract
PURPOSE OF REVIEW Childhood asthma is a heterogeneous disease and many children have uncontrolled disease. Therefore an individualized approach is needed to improve asthma outcomes in children. Precision medicine using clinical characteristics, biomarkers, and the rapidly involving field of genomics and pharmacogenomics aims to achieve asthma control and reduce future risks with less side-effects in individual children with asthma. RECENT FINDINGS It is not yet possible to select treatment options on clinical characteristics. Novel monoclonal antibodies are efficacious in patients with severe, eosinophilic asthma. Reduced lung function growth and early decline is a prevalent finding in children with persistent asthma. Pharmacogenetic studies have identified children at risk for cortisol suppression when using inhaled corticosteroids. SUMMARY Clinical characteristics and simple biomarkers like eosinophils, IgE, and the fraction of exhaled nitric oxide may be used in clinical practice for a basic precision medicine approach, deciding which children will have the best chance to respond to inhaled corticosteroids and to the biologicals omalizumab and mepolizumab.Further application of pharmacogenomics and breathomics needs additional studies before they can be applied as tools for precision medicine in individual children with asthma.
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Bentley AR, Callier SL, Rotimi CN. Evaluating the promise of inclusion of African ancestry populations in genomics. NPJ Genom Med 2020; 5:5. [PMID: 32140257 PMCID: PMC7042246 DOI: 10.1038/s41525-019-0111-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022] Open
Abstract
The lack of representation of diverse ancestral backgrounds in genomic research is well-known, and the resultant scientific and ethical limitations are becoming increasingly appreciated. The paucity of data on individuals with African ancestry is especially noteworthy as Africa is the birthplace of modern humans and harbors the greatest genetic diversity. It is expected that greater representation of those with African ancestry in genomic research will bring novel insights into human biology, and lead to improvements in clinical care and improved understanding of health disparities. Now that major efforts have been undertaken to address this failing, is there evidence of these anticipated advances? Here, we evaluate the promise of including diverse individuals in genomic research in the context of recent literature on individuals of African ancestry. In addition, we discuss progress and achievements on related technological challenges and diversity among scientists conducting genomic research.
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Affiliation(s)
- Amy R. Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Shawneequa L. Callier
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
- Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC USA
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
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56
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Abstract
The majority of studies of genetic association with disease have been performed in Europeans. This European bias has important implications for risk prediction of diseases across global populations. In this commentary, we justify the need to study more diverse populations using both empirical examples and theoretical reasoning.
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Affiliation(s)
- Giorgio Sirugo
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Scott M Williams
- Departments of Population and Quantitative Health Sciences, and Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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57
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Kabesch M, Tost J. Recent findings in the genetics and epigenetics of asthma and allergy. Semin Immunopathol 2020; 42:43-60. [PMID: 32060620 PMCID: PMC7066293 DOI: 10.1007/s00281-019-00777-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 12/22/2019] [Indexed: 12/16/2022]
Abstract
In asthma and allergy genetics, a trend towards a few main topics developed over the last 2 years. First, a number of studies have been published recently which focus on overlapping and/or very specific phenotypes: within the allergy spectrum but also reaching beyond, looking for common genetic traits shared between different diseases or disease entities. Secondly, an urgently needed focus has been put on asthma and allergy genetics in populations genetically different from European ancestry. This acknowledges that the majority of new asthma patients today are not white and asthma is a truly worldwide disease. In epigenetics, recent years have seen several large-scale epigenome-wide association studies (EWAS) being published and a further focus was on the interaction between the environment and epigenetic signatures. And finally, the major trends in current asthma and allergy genetics and epigenetics comes from the field of pharmacogenetics, where it is necessary to understand the susceptibility for and mechanisms of current asthma and allergy therapies while at the same time, we need to have scientific answers to the recent availability of novel drugs that hold the promise for a more individualized therapy.
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Affiliation(s)
- Michael Kabesch
- Department of Pediatric Pneumology and Allergy, St. Hedwig's Hospital of the order of St. John, University Children's Hospital Regensburg (KUNO), Steinmetzstr. 1-3, 93049, Regensburg, Germany.
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, 2 rue Gaston Crémieux, 91000, Evry, France
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Abstract
PURPOSE OF REVIEW Asthma exacerbations have been suggested to result from complex interactions between genetic and nongenetic components. In this review, we provide an overview of the genetic association studies of asthma exacerbations, their main results and limitations, as well as future directions of this field. RECENT FINDINGS Most studies on asthma exacerbations have been performed using a candidate-gene approach. Although few genome-wide association studies of asthma exacerbations have been conducted up to date, they have revealed promising associations but with small effect sizes. Additionally, the analysis of interactions between genetic and environmental factors has contributed to better understand of genotype-specific responses in asthma exacerbations. SUMMARY Genetic association studies have allowed identifying the 17q21 locus and the ADRB2 gene as the loci most consistently associated with asthma exacerbations. Future studies should explore the full spectrum of genetic variation and will require larger sample sizes, a better representation of racial/ethnic diversity and a more precise definition of asthma exacerbations. Additionally, the analysis of important environmental gene-environment analysis and the integration of multiple omics will allow understanding the genetic factors and biological processes underlying the risk for asthma exacerbations.
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59
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Zhang E, Levin AM, Williams LK. How does race and ethnicity effect the precision treatment of asthma? EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2019; 4:337-356. [PMID: 33015363 DOI: 10.1080/23808993.2019.1690396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction Asthma is a common condition that affects large numbers of children and adults, yet the burden of disease is not equally distributed amongst groups. In the United States, African Americans and Puerto Ricans have higher rates of asthma and its complications when compared with European Americans. However, clinical trials and genetic studies have largely focused on the latter group. Areas covered Here we examine what is known regarding differences in asthma treatment response by race-ethnicity. We also review existing genetic studies related to the use of asthma medications, paying special attention to studies that included substantial numbers of non-white population groups. Publicly accessible search engines of the medical literature were queried using combinations of the terms asthma, race, ethnicity, pharmacogenomics, and pharmacogenetics, as well as the names of individual asthma medication classes. The list of articles reviewed was supplemented by bibliographies and expert knowledge. Expert opinion A substantial and coordinated effort is still needed to both identify and validate genetic biomarkers of asthma medication response, as currently there are no clinically actionable genetic markers available for this purpose. The path to identifying such markers in non-white populations is even more formidable, since these groups are underrepresented in existing data.
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Affiliation(s)
- Ellen Zhang
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
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60
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Schoettler N, Rodríguez E, Weidinger S, Ober C. Advances in asthma and allergic disease genetics: Is bigger always better? J Allergy Clin Immunol 2019; 144:1495-1506. [PMID: 31677964 DOI: 10.1016/j.jaci.2019.10.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022]
Abstract
This review focuses on genome-wide association studies (GWASs) of asthma and allergic diseases published between January 1, 2018, and June 30, 2019. During this time period, there were 38 GWASs reported in 19 articles, including the largest performed to date for many of these conditions. Overall, we learned that childhood-onset asthma is associated with the most independent loci compared with other defined groups of asthma and allergic disease cases; adult-onset asthma and moderate-to-severe asthma are associated with fewer genes, which are largely a subset of those associated with childhood-onset asthma. There is significant genetic overlap between asthma and allergic diseases, particularly with respect to childhood-onset asthma, which involves genes that reflect the importance of barrier function biology, and to HLA region genes, which are the most frequently associated genes overall in both groups of diseases. Although the largest GWASs in African American and Latino/Hispanic populations were reported during this period, they are still significantly underpowered compared with studies reported in populations of European ancestry, highlighting the need for larger studies, particularly in patients with childhood-onset asthma and allergic diseases, in these important populations that carry the greatest burden of disease.
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Affiliation(s)
- Nathan Schoettler
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, Ill; Department of Human Genetics, University of Chicago, Chicago, Ill.
| | - Elke Rodríguez
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
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61
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Thorn CF, Whirl-Carrillo M, Hachad H, Johnson JA, McDonagh EM, Ratain MJ, Relling MV, Scott SA, Altman RB, Klein TE. Essential Characteristics of Pharmacogenomics Study Publications. Clin Pharmacol Ther 2019; 105:86-91. [PMID: 30406943 DOI: 10.1002/cpt.1279] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/02/2018] [Indexed: 12/17/2022]
Abstract
Pharmacogenomics (PGx) can be seen as a model for biomedical studies: it includes all disease areas of interest and spans in vitro studies to clinical trials, while focusing on the relationships between genes and drugs and the resulting phenotypes. This review will examine different characteristics of PGx study publications and provide examples of excellence in framing PGx questions and reporting their resulting data in a way that maximizes the knowledge that can be built on them.
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Affiliation(s)
- Caroline F Thorn
- Department of Biomedical Data Sciences, Stanford University, Stanford, California, USA
| | | | - Houda Hachad
- Translational Software, Bellevue, Washington, USA
| | - Julie A Johnson
- College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | | | - Mark J Ratain
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Mary V Relling
- Pharmaceutical Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, a Mount Sinai Venture, Stamford, Connecticut, USA
| | - Russ B Altman
- Department of Genetics, Department of Computer Science, Department of Biomedical Engineering, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Sciences, Stanford University, Stanford, California, USA
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62
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Szpiech ZA, Mak ACY, White MJ, Hu D, Eng C, Burchard EG, Hernandez RD. Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity. Am J Hum Genet 2019; 105:747-762. [PMID: 31543216 PMCID: PMC6817522 DOI: 10.1016/j.ajhg.2019.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
Runs of homozygosity (ROH) are important genomic features that manifest when an individual inherits two haplotypes that are identical by descent. Their length distributions are informative about population history, and their genomic locations are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. We have previously shown that ROH, and especially long ROH that are likely the result of recent parental relatedness, are enriched for homozygous deleterious coding variation in a worldwide sample of outbred individuals. However, the distribution of ROH in admixed populations and their relationship to deleterious homozygous genotypes is understudied. Here we analyze whole-genome sequencing data from 1,441 unrelated individuals from self-identified African American, Puerto Rican, and Mexican American populations. These populations are three-way admixed between European, African, and Native American ancestries and provide an opportunity to study the distribution of deleterious alleles partitioned by local ancestry and ROH. We re-capitulate previous findings that long ROH are enriched for deleterious variation genome-wide. We then partition by local ancestry and show that deleterious homozygotes arise at a higher rate when ROH overlap African ancestry segments than when they overlap European or Native American ancestry segments of the genome. These results suggest that, while ROH on any haplotype background are associated with an inflation of deleterious homozygous variation, African haplotype backgrounds may play a particularly important role in the genetic architecture of complex diseases for admixed individuals, highlighting the need for further study of these populations.
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Affiliation(s)
- Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Department of Biological Sciences, Auburn University, Auburn, AL 36842, USA.
| | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marquitta J White
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada; Genome Quebec Innovation Center, McGill University, Montreal, QC H3A 0G1, Canada.
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63
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Nebert DW, Liu Z. SLC39A8 gene encoding a metal ion transporter: discovery and bench to bedside. Hum Genomics 2019; 13:51. [PMID: 31521203 PMCID: PMC6744627 DOI: 10.1186/s40246-019-0233-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/14/2019] [Indexed: 01/08/2023] Open
Abstract
SLC39A8 is an evolutionarily highly conserved gene that encodes the ZIP8 metal cation transporter in all vertebrates. SLC39A8 is ubiquitously expressed, including pluripotent embryonic stem cells; SLC39A8 expression occurs in every cell type examined. Uptake of ZIP8-mediated Mn2+, Zn2+, Fe2+, Se4+, and Co2+ represents endogenous functions-moving these cations into the cell. By way of mouse genetic differences, the phenotype of "subcutaneous cadmium-induced testicular necrosis" was assigned to the Cdm locus in the 1970s. This led to identification of the mouse Slc39a8 gene, its most closely related Slc39a14 gene, and creation of Slc39a8-overexpressing, Slc39a8(neo/neo) knockdown, and cell type-specific conditional knockout mouse lines; the Slc39a8(-/-) global knockout mouse is early-embryolethal. Slc39a8(neo/neo) hypomorphs die between gestational day 16.5 and postnatal day 1-exhibiting severe anemia, dysregulated hematopoiesis, hypoplastic spleen, dysorganogenesis, stunted growth, and hypomorphic limbs. Not surprisingly, genome-wide association studies subsequently revealed human SLC39A8-deficiency variants exhibiting striking pleiotropy-defects correlated with clinical disorders in virtually every organ, tissue, and cell-type: numerous developmental and congenital disorders, the immune system, cardiovascular system, kidney, lung, liver, coagulation system, central nervous system, musculoskeletal system, eye, and gastrointestinal tract. Traits with which SLC39A8-deficiency variants are currently associated include Mn2+-deficient hypoglycosylation; numerous birth defects; Leigh syndrome-like mitochondrial redox deficiency; decreased serum high-density lipoprotein-cholesterol levels; increased body mass index; greater risk of coronary artery disease, hypotension, cardiovascular death, allergy, ischemic stroke, schizophrenia, Parkinson disease, inflammatory bowel disease, Crohn disease, myopia, and adolescent idiopathic scoliosis; systemic lupus erythematosus with primary Sjögren syndrome; decreased height; and inadvertent participation in the inflammatory progression of osteoarthritis.
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Affiliation(s)
- Daniel W Nebert
- Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati Medical Center, Cincinnati, OH, 45267-0056, USA.
- Division of Human Genetics, Department of Pediatrics & Molecular Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, 45229-2899, USA.
| | - Zijuan Liu
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA
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Lorenzo-Salazar JM, Flores C. Assessing Asthma Medication Responses in U.S. Minority Children by Whole-Genome Sequencing. Am J Respir Crit Care Med 2019; 197:1513-1514. [PMID: 29578752 DOI: 10.1164/rccm.201803-0457ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Carlos Flores
- 1 Instituto Tecnológico y de Energías Renovables Tenerife, Spain.,2 CIBER de Enfermedades Respiratorias Instituto de Salud Carlos III Madrid, Spain and.,3 Research Unit Hospital Universitario Nuestra Señora de Candelaria Tenerife, Spain
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65
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Geng X, Liu L, Banes-Berceli A, Yang Z, Kang P, Shen J, Tsai KJ, Liu Z. Role of ZIP8 in regulating cell morphology and NF-κB/Snail2 signaling. Metallomics 2019; 10:953-964. [PMID: 29927450 DOI: 10.1039/c8mt00079d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ZIP8 is a recently identified membrane transporter which facilitates uptake of many substrates including both essential and toxic divalent metals (e.g. zinc, manganese, iron, cadmium) and inorganic selenium. Many ZIP8 regulated downstream signals and pathways remain to be elucidated. In this study, we investigated ZIP8 regulatory roles in downstream targets in ZIP8-gain and loss cells and in ZIP8 overexpressed lungs. Our results show that the overexpression of ZIP8 in mouse fibroblast cells (MEF) induces significant morphological change and re-organization of filament actin (F-actin), along with increased cell proliferation and migration rate. In ZIP8 knockout chronic myelogenous leukemia HAP1 cells, significant clonal morphological change with increased cell-cell adhesion was observed. In the ZIP8 overexpressed lung, F-actin was aberrantly enriched around the tracheal branch. In these ZIP8 gain and loss cell lines and ZIP8 transgenic lungs, we identified two relevant transcription factors, NF-κB and Snail2, whose activation is dependent on the ZIP8 level. They were both significantly upregulated in ZIP8 overexpressed cells and lungs. Expression of NF-κB and Snail2 targets, COL1A2 and E-cadherin, was also correspondingly elevated. Taken together, our results suggest that ZIP8 is a new regulator for cell morphology and cytoskeleton which involves NF-κB and Snail2.
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Affiliation(s)
- Xiangrong Geng
- Department of Biological Sciences, Oakland University, 2200 N. Squirrel Rd, Rochester, MI 48309, USA.
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66
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Chartier KG. The paucity of genetic studies of alcohol phenotypes in diverse populations: what are the consequences and opportunities? Addiction 2019; 114:1147-1149. [PMID: 30537438 DOI: 10.1111/add.14524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/19/2018] [Accepted: 11/27/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Karen G Chartier
- School of Social Work, Virginia Commonwealth University, Richmond, VA, USA.,Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
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67
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Portman MA, Dahdah NS, Slee A, Olson AK, Choueiter NF, Soriano BD, Buddhe S, Altman CA. Etanercept With IVIg for Acute Kawasaki Disease: A Randomized Controlled Trial. Pediatrics 2019; 143:peds.2018-3675. [PMID: 31048415 PMCID: PMC6564061 DOI: 10.1542/peds.2018-3675] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/11/2019] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Patients with Kawasaki disease can develop life-altering coronary arterial abnormalities, particularly in those resistant to intravenous immunoglobulin (IVIg) therapy. We tested the tumor necrosis factor α receptor antagonist etanercept for reducing both IVIg resistance and coronary artery (CA) disease progression. METHODS In a double-blind multicenter trial, patients with Kawasaki disease received either etanercept (0.8 mg/kg; n = 100) or placebo (n = 101) subcutaneously starting immediately after IVIg infusion. IVIg resistance was the primary outcome with prespecified subgroup analyses according to age, sex, and race. Secondary outcomes included echocardiographic CA measures within subgroups defined by coronary dilation (z score >2.5) at baseline. We used generalized estimating equations to analyze z score change and a prespecified algorithm for change in absolute diameters. RESULTS IVIg resistance occurred in 22% (placebo) and 13% (etanercept) of patients (P = .10). Etanercept reduced IVIg resistance in patients >1 year of age (P = .03). In the entire population, 46 (23%) had a coronary z score >2.5 at baseline. Etanercept reduced coronary z score change in those with and without baseline dilation (P = .04 and P = .001); no improvement occurred in the analogous placebo groups. Etanercept (n = 22) reduced dilation progression compared with placebo (n = 24) by algorithm in those with baseline dilation (P = .03). No difference in the safety profile occurred between etanercept and placebo. CONCLUSIONS Etanercept showed no significant benefit in IVIg resistance in the entire population. However, preplanned analyses showed benefit in patients >1 year. Importantly, etanercept appeared to ameliorate CA dilation, particularly in patients with baseline abnormalities.
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Affiliation(s)
- Michael A. Portman
- Seattle Children’s Research Institute, School
of Medicine, University of Washington, Seattle, Washington
| | - Nagib S. Dahdah
- Sainte Justine University Hospital Center, University
of Montreal, Montreal, Canada
| | | | - Aaron K. Olson
- Seattle Children’s Research Institute, School
of Medicine, University of Washington, Seattle, Washington
| | - Nadine F. Choueiter
- Montefiore Children’s Hospital, Albert
Einstein College of Medicine, Bronx, New York; and
| | - Brian D. Soriano
- Seattle Children’s Research Institute, School
of Medicine, University of Washington, Seattle, Washington
| | - Sujatha Buddhe
- Seattle Children’s Research Institute, School
of Medicine, University of Washington, Seattle, Washington
| | - Carolyn A. Altman
- Texas Children’s Hospital, Baylor College of
Medicine, Houston, Texas
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Vergara C, Thio CL, Johnson E, Kral AH, O'Brien TR, Goedert JJ, Mangia A, Piazzolla V, Mehta SH, Kirk GD, Kim AY, Lauer GM, Chung RT, Cox AL, Peters MG, Khakoo SI, Alric L, Cramp ME, Donfield SM, Edlin BR, Busch MP, Alexander G, Rosen HR, Murphy EL, Latanich R, Wojcik GL, Taub MA, Valencia A, Thomas DL, Duggal P. Multi-Ancestry Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus. Gastroenterology 2019; 156:1496-1507.e7. [PMID: 30593799 PMCID: PMC6788806 DOI: 10.1053/j.gastro.2018.12.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/05/2018] [Accepted: 12/19/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Spontaneous clearance of hepatitis C virus (HCV) occurs in approximately 30% of infected persons and less often in populations of African ancestry. Variants in major histocompatibility complex (MHC) and in interferon lambda genes are associated with spontaneous HCV clearance, but there have been few studies of these variants in persons of African ancestry. We performed a dense multi-ancestry genome-wide association study of spontaneous clearance of HCV, focusing on individuals of African ancestry. METHODS We performed genotype analyses of 4423 people from 3 ancestry groups: 2201 persons of African ancestry (445 with HCV clearance and 1756 with HCV persistence), 1739 persons of European ancestry (701 with HCV clearance and 1036 with HCV persistence), and 486 multi-ancestry Hispanic persons (173 with HCV clearance and 313 with HCV persistence). Samples were genotyped using Illumina (San Diego, CA) arrays and statistically imputed to the 1000 Genomes Project. For each ancestry group, the association of single-nucleotide polymorphisms with HCV clearance was tested by log-additive analysis, and then a meta-analysis was performed. RESULTS In the meta-analysis, significant associations with HCV clearance were confirmed at the interferon lambda gene locus IFNL4-IFNL3 (19q13.2) (P = 5.99 × 10-50) and the MHC locus 6p21.32 (P = 1.15 × 10-21). We also associated HCV clearance with polymorphisms in the G-protein-coupled receptor 158 gene (GPR158) at 10p12.1 (P = 1.80 × 10-07). These 3 loci had independent, additive effects of HCV clearance, and account for 6.8% and 5.9% of the variance of HCV clearance in persons of European and African ancestry, respectively. Persons of African or European ancestry carrying all 6 variants were 24-fold and 11-fold, respectively, more likely to clear HCV infection compared with individuals carrying none or 1 of the clearance-associated variants. CONCLUSIONS In a meta-analysis of data from 3 studies, we found variants in MHC genes, IFNL4-IFNL3, and GPR158 to increase odds of HCV clearance in patients of European and African ancestry. These findings could increase our understanding of immune response to and clearance of HCV infection.
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Affiliation(s)
| | - Chloe L Thio
- Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Eric Johnson
- Research Triangle Institute International, Research Triangle Park, North Carolina; Atlanta, Georgia; San Francisco, California
| | - Alex H Kral
- Research Triangle Institute International, Research Triangle Park, North Carolina; Atlanta, Georgia; San Francisco, California
| | - Thomas R O'Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - James J Goedert
- Liver Unit Istituto Di Ricovero e Cura a Carattere Scientifico "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Alessandra Mangia
- Liver Unit Istituto Di Ricovero e Cura a Carattere Scientifico "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Valeria Piazzolla
- Liver Unit Istituto Di Ricovero e Cura a Carattere Scientifico "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Shruti H Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland
| | - Gregory D Kirk
- Johns Hopkins University, School of Medicine, Baltimore, Maryland; Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland
| | - Arthur Y Kim
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Andrea L Cox
- Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Marion G Peters
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, California
| | - Salim I Khakoo
- University of Southampton, Southampton General Hospital, Southampton, UK
| | - Laurent Alric
- Department of Internal Medicine and Digestive Diseases, Centre Hospitalier Universitaire Purpan, UMR 152, Institut de Recherche pour le Développement Toulouse 3 University, France
| | | | | | - Brian R Edlin
- State University of New York Downstate College of Medicine, Brooklyn, New York
| | - Michael P Busch
- University of California and Vitalant Research Institute, San Francisco, California
| | - Graeme Alexander
- University College London Institute for Liver and Digestive Health, The Royal Free Hospital, London, UK
| | | | - Edward L Murphy
- University of California and Vitalant Research Institute, San Francisco, California
| | - Rachel Latanich
- Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Genevieve L Wojcik
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Margaret A Taub
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland
| | - Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, Maryland; Universidad Pontificia Bolivariana, Medellin, Colombia
| | - David L Thomas
- Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland.
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Bilkey GA, Burns BL, Coles EP, Bowman FL, Beilby JP, Pachter NS, Baynam G, J. S. Dawkins H, Nowak KJ, Weeramanthri TS. Genomic Testing for Human Health and Disease Across the Life Cycle: Applications and Ethical, Legal, and Social Challenges. Front Public Health 2019; 7:40. [PMID: 30915323 PMCID: PMC6421958 DOI: 10.3389/fpubh.2019.00040] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/14/2019] [Indexed: 12/23/2022] Open
Abstract
The expanding use of genomic technologies encompasses all phases of life, from the embryo to the elderly, and even the posthumous phase. In this paper, we present the spectrum of genomic healthcare applications, and describe their scope and challenges at different stages of the life cycle. The integration of genomic technology into healthcare presents unique ethical issues that challenge traditional aspects of healthcare delivery. These challenges include the different definitions of utility as applied to genomic information; the particular characteristics of genetic data that influence how it might be protected, used and shared; and the difficulties applying existing models of informed consent, and how new consent models might be needed.
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Affiliation(s)
- Gemma A. Bilkey
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, East Perth, WA, Australia
- Office of the Chief Health Officer, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, East Perth, WA, Australia
| | - Belinda L. Burns
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, East Perth, WA, Australia
| | - Emily P. Coles
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, East Perth, WA, Australia
| | - Faye L. Bowman
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, East Perth, WA, Australia
| | - John P. Beilby
- PathWest Laboratory Medicine, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
- Faculty of Health and Medical Sciences, School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Nicholas S. Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Department of Health, Government of Western Australia, Subiaco, WA, Australia
- Faculty of Health and Medical Sciences, School of Medicine, The University of Western Australia, Crawley, WA, Australia
| | - Gareth Baynam
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, East Perth, WA, Australia
- Genetic Services of Western Australia, King Edward Memorial Hospital, Department of Health, Government of Western Australia, Subiaco, WA, Australia
- Faculty of Health and Medical Sciences, School of Medicine, The University of Western Australia, Crawley, WA, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Department of Health, Government of Western Australia, Subiaco, WA, Australia
- Centre for Child Health Research, The University of Western Australia and Telethon Kids Institute, Perth, WA, Australia
| | - Hugh J. S. Dawkins
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, East Perth, WA, Australia
- Faculty of Health and Medical Sciences, School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Sir Walter Murdoch School of Policy and International Affairs, Murdoch University, Murdoch, WA, Australia
- School of Public Health, Curtin University of Technology, Bentley, WA, Australia
| | - Kristen J. Nowak
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, East Perth, WA, Australia
- Faculty of Health and Medical Sciences, School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Tarun S. Weeramanthri
- Office of the Chief Health Officer, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, East Perth, WA, Australia
- Faculty of Health and Medical Sciences, School of Population and Global Health, The University of Western Australia, Crawley, WA, Australia
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Belcher A, Mangelsdorf M, McDonald F, Curtis C, Waddell N, Hussey K. What does Australia's investment in genomics mean for public health? Aust N Z J Public Health 2019; 43:204-206. [PMID: 30830712 DOI: 10.1111/1753-6405.12887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
| | | | - Fiona McDonald
- Australian Centre for Health Law Research, Queensland University of Technology
| | | | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Queensland
| | - Karen Hussey
- Centre for Policy Futures, The University of Queensland
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Lauschke VM, Ingelman-Sundberg M. Prediction of drug response and adverse drug reactions: From twin studies to Next Generation Sequencing. Eur J Pharm Sci 2019; 130:65-77. [PMID: 30684656 DOI: 10.1016/j.ejps.2019.01.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 01/12/2023]
Abstract
Understanding and predicting inter-individual differences related to the success of drug therapy is of tremendous importance, both during drug development and for clinical applications. Importantly, while seminal twin studies indicate that the majority of inter-individual differences in drug disposition are driven by hereditary factors, common genetic polymorphisms explain only less than half of this genetically encoded variability. Recent progress in Next Generation Sequencing (NGS) technologies has for the first time allowed to comprehensively map the genetic landscape of human pharmacogenes. Importantly, these projects have unveiled vast numbers of rare genetic variants, which are estimated to contribute substantially to the missing heritability of drug metabolism phenotypes. However, functional interpretation of these rare variants remains challenging and constitutes one of the important frontiers of contemporary pharmacogenomics. Furthermore, NGS technologies face challenges in the interrogation of genes residing in complex genomic regions, such as CYP2D6 and HLA genes. We here provide an update of the implementation of pharmacogenomic variations in the clinical setting and present emerging strategies that facilitate the translation of NGS data into clinically useful information. Importantly, we anticipate that these developments will soon result in a paradigm shift of pre-emptive genotyping away from the interrogation to candidate variants and towards the comprehensive profiling of an individuals genotype, thus allowing for a true individualization of patient drug treatment regimens.
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Affiliation(s)
- Volker M Lauschke
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
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Hernandez-Pacheco N, Pino-Yanes M, Flores C. Genomic Predictors of Asthma Phenotypes and Treatment Response. Front Pediatr 2019; 7:6. [PMID: 30805318 PMCID: PMC6370703 DOI: 10.3389/fped.2019.00006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
Asthma is a complex respiratory disease considered as the most common chronic condition in children. A large genetic contribution to asthma susceptibility is predicted by the clustering of asthma and allergy symptoms among relatives and the large disease heritability estimated from twin studies, ranging from 55 to 90%. Genetic basis of asthma has been extensively investigated in the past 40 years using linkage analysis and candidate-gene association studies. However, the development of dense arrays for polymorphism genotyping has enabled the transition toward genome-wide association studies (GWAS), which have led the discovery of several unanticipated asthma genes in the last 11 years. Despite this, currently known risk variants identified using many thousand samples from distinct ethnicities only explain a small proportion of asthma heritability. This review examines the main findings of the last 2 years in genomic studies of asthma using GWAS and admixture mapping studies, as well as the direction of studies fostering integrative perspectives involving omics data. Additionally, we discuss the need for assessing the whole spectrum of genetic variation in association studies of asthma susceptibility, severity, and treatment response in order to further improve our knowledge of asthma genes and predictive biomarkers. Leveraging the individual's genetic information will allow a better understanding of asthma pathogenesis and will facilitate the transition toward a more precise diagnosis and treatment.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
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Louisias M, Wright L, Phipatanakul W. Asthma in the melting pot. Ann Allergy Asthma Immunol 2018; 122:136-139. [PMID: 30465857 DOI: 10.1016/j.anai.2018.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/03/2018] [Accepted: 11/08/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Margee Louisias
- Boston Children's Hospital, Division of Allergy and Immunology, Boston, Massachusetts; Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Lakiea Wright
- Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Wanda Phipatanakul
- Boston Children's Hospital, Division of Allergy and Immunology, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts.
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75
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Rashkin SR, Chua KC, Ho C, Mulkey F, Jiang C, Mushiroda T, Kubo M, Friedman PN, Rugo HS, McLeod HL, Ratain MJ, Castillos F, Naughton M, Overmoyer B, Toppmeyer D, Witte JS, Owzar K, Kroetz DL. A Pharmacogenetic Prediction Model of Progression-Free Survival in Breast Cancer using Genome-Wide Genotyping Data from CALGB 40502 (Alliance). Clin Pharmacol Ther 2018; 105:738-745. [PMID: 30260474 DOI: 10.1002/cpt.1241] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/30/2018] [Indexed: 01/10/2023]
Abstract
Genome-wide genotyping data are increasingly available for pharmacogenetic association studies, but application of these data for development of prediction models is limited. Prediction methods, such as elastic net regularization, have recently been applied to genetic studies but only limitedly to pharmacogenetic outcomes. An elastic net was applied to a pharmacogenetic study of progression-free survival (PFS) of 468 patients with advanced breast cancer in a clinical trial of paclitaxel, nab-paclitaxel, and ixabepilone. A final model included 13 single nucleotide polymorphisms (SNPs) in addition to clinical covariates (prior taxane status, hormone receptor status, disease-free interval, and presence of visceral metastases) with an area under the curve (AUC) integrated over time of 0.81, an increase compared to an AUC of 0.64 for a model with clinical covariates alone. This model may be of value in predicting PFS with microtubule targeting agents and may inform reverse translational studies to understand differential response to these drugs.
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Affiliation(s)
- Sara R Rashkin
- Department of Biostatistics and Epidemiology, University of California San Francisco, San Francisco, California, USA
| | - Katherina C Chua
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Carol Ho
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Flora Mulkey
- Alliance Statistics and Data Center, Duke University, Durham, North Carolina, USA
| | - Chen Jiang
- Alliance Statistics and Data Center, Duke University, Durham, North Carolina, USA
| | - Tasei Mushiroda
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Paula N Friedman
- Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hope S Rugo
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, Florida, USA
| | - Mark J Ratain
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | | | - Michael Naughton
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Beth Overmoyer
- Dana-Farber/Partners Cancer Care, Boston, Massachusetts, USA
| | - Deborah Toppmeyer
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - John S Witte
- Department of Biostatistics and Epidemiology, University of California San Francisco, San Francisco, California, USA
| | - Kouros Owzar
- Alliance Statistics and Data Center, Duke University, Durham, North Carolina, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
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Role of ZIP8 in regulation of cisplatin sensitivity through Bcl-2. Toxicol Appl Pharmacol 2018; 362:52-58. [PMID: 30342059 DOI: 10.1016/j.taap.2018.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/12/2018] [Accepted: 10/16/2018] [Indexed: 02/06/2023]
Abstract
ZIP8 is a membrane transporter that facilitates the uptake of divalent metals (e.g., Zn, Mn, Fe, Cd) and the mineral selenite in anionic form. ZIP8 functionality has been recently reported to regulate cell proliferation, migration and cytoskeleton arrangement, exhibiting an essential role for normal physiology. In this study, we report a ZIP8 role in chemotherapy response. We show ZIP8 regulates cell sensitivity to the anti-cancer drug cisplatin. Overexpression of ZIP8 in mouse embryonic fibroblast (MEF) cells induces cisplatin sensitivity, while knockout of ZIP8 in leukemia HAP1 cells leads to cisplatin resistance. In ZIP8 altered cells and transgenic mice, we show cisplatin is not a direct ZIP8 substrate. Further studies demonstrate that ZIP8 regulates anti-apoptotic protein Bcl-2. ZIP8 overexpression decreases Bcl-2 levels in cultured cells, mice lung and liver tissue while loss of ZIP8 elevates Bcl-2 expression in HAP1 cells and liver tissue. We also observe that ZIP8 overexpression modulates cisplatin-induced cell apoptosis, manifested by the increased protein level of cleaved Caspase-3. Since Bcl-2 elevation was previously discovered to induce cisplatin drug resistance, our results suggest ZIP8 may modulate cisplatin drug responses as well as apoptosis through Bcl-2. We therefore conclude ZIP8 is a new molecule to be involved in cisplatin drug responses and is predicted as a genetic factor to be considered in cisplatin therapy.
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De T, Park CS, Perera MA. Cardiovascular Pharmacogenomics: Does It Matter If You're Black or White? Annu Rev Pharmacol Toxicol 2018; 59:577-603. [PMID: 30296897 DOI: 10.1146/annurev-pharmtox-010818-021154] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Race and ancestry have long been associated with differential risk and outcomes to disease as well as responses to medications. These differences in drug response are multifactorial with some portion associated with genomic variation. The field of pharmacogenomics aims to predict drug response in patients prior to medication administration and to uncover the biological underpinnings of drug response. The field of human genetics has long recognized that genetic variation differs in frequency between ancestral populations, with some single nucleotide polymorphisms found solely in one population. Thus far, most pharmacogenomic studies have focused on individuals of European and East Asian ancestry, resulting in a substantial disparity in the clinical utility of genetic prediction for drug response in US minority populations. In this review, we discuss the genetic factors that underlie variability to drug response and known pharmacogenomic associations and how these differ between populations, with an emphasis on the current knowledge in cardiovascular pharmacogenomics.
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Affiliation(s)
- Tanima De
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA;
| | - C Sehwan Park
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA;
| | - Minoli A Perera
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA;
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Mead TJ, Apte SS. ADAMTS proteins in human disorders. Matrix Biol 2018; 71-72:225-239. [PMID: 29885460 DOI: 10.1016/j.matbio.2018.06.002] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 02/07/2023]
Abstract
ADAMTS proteins are a superfamily of 26 secreted molecules comprising two related, but distinct families. ADAMTS proteases are zinc metalloendopeptidases, most of whose substrates are extracellular matrix (ECM) components, whereas ADAMTS-like proteins lack a metalloprotease domain, reside in the ECM and have regulatory roles vis-à-vis ECM assembly and/or ADAMTS activity. Evolutionary conservation and expansion of ADAMTS proteins in mammals is suggestive of crucial embryologic or physiological roles in humans. Indeed, Mendelian disorders or birth defects resulting from naturally occurring ADAMTS2, ADAMTS3, ADAMTS10, ADAMTS13, ADAMTS17, ADAMTS20, ADAMTSL2 and ADAMTSL4 mutations as well as numerous phenotypes identified in genetically engineered mice have revealed ADAMTS participation in major biological pathways. Important roles have been identified in a few acquired conditions. ADAMTS5 is unequivocally implicated in pathogenesis of osteoarthritis via degradation of aggrecan, a major structural proteoglycan in cartilage. ADAMTS7 is strongly associated with coronary artery disease and promotes atherosclerosis. Autoantibodies to ADAMTS13 lead to a platelet coagulopathy, thrombotic thrombocytopenic purpura, which is similar to that resulting from ADAMTS13 mutations. ADAMTS proteins have numerous potential connections to other human disorders that were identified by genome-wide association studies. Here, we review inherited and acquired human disorders in which ADAMTS proteins participate, and discuss progress and prospects in therapeutics.
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Affiliation(s)
- Timothy J Mead
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, United States
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, United States.
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