1
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Chan LE, Casiraghi E, Reese J, Harmon QE, Schaper K, Hegde H, Valentini G, Schmitt C, Motsinger-Reif A, Hall JE, Mungall CJ, Robinson PN, Haendel MA. Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests. Int J Med Inform 2024; 187:105461. [PMID: 38643701 DOI: 10.1016/j.ijmedinf.2024.105461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 04/23/2024]
Abstract
OBJECTIVE Female reproductive disorders (FRDs) are common health conditions that may present with significant symptoms. Diet and environment are potential areas for FRD interventions. We utilized a knowledge graph (KG) method to predict factors associated with common FRDs (for example, endometriosis, ovarian cyst, and uterine fibroids). MATERIALS AND METHODS We harmonized survey data from the Personalized Environment and Genes Study (PEGS) on internal and external environmental exposures and health conditions with biomedical ontology content. We merged the harmonized data and ontologies with supplemental nutrient and agricultural chemical data to create a KG. We analyzed the KG by embedding edges and applying a random forest for edge prediction to identify variables potentially associated with FRDs. We also conducted logistic regression analysis for comparison. RESULTS Across 9765 PEGS respondents, the KG analysis resulted in 8535 significant or suggestive predicted links between FRDs and chemicals, phenotypes, and diseases. Amongst these links, 32 were exact matches when compared with the logistic regression results, including comorbidities, medications, foods, and occupational exposures. DISCUSSION Mechanistic underpinnings of predicted links documented in the literature may support some of our findings. Our KG methods are useful for predicting possible associations in large, survey-based datasets with added information on directionality and magnitude of effect from logistic regression. These results should not be construed as causal but can support hypothesis generation. CONCLUSION This investigation enabled the generation of hypotheses on a variety of potential links between FRDs and exposures. Future investigations should prospectively evaluate the variables hypothesized to impact FRDs.
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Affiliation(s)
- Lauren E Chan
- Oregon State University, College of Public Health and Human Sciences, Corvallis, OR, USA.
| | - Elena Casiraghi
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; European Laboratory for Learning and Intelligent Systems, ELLIS
| | - Justin Reese
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Quaker E Harmon
- National Institute of Environmental Health Sciences, Epidemiology Branch, Durham, NC, USA
| | - Kevin Schaper
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Harshad Hegde
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Giorgio Valentini
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy; European Laboratory for Learning and Intelligent Systems, ELLIS
| | - Charles Schmitt
- National Institute of Environmental Health Sciences, Office of Data Science, Durham, NC, USA
| | - Alison Motsinger-Reif
- National Institute of Environmental Health Sciences, Biostatistics & Computational Biology Branch, Durham, NC, USA
| | - Janet E Hall
- National Institute of Environmental Health Sciences, Clinical Research Branch, Durham, NC, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Peter N Robinson
- European Laboratory for Learning and Intelligent Systems, ELLIS; The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Melissa A Haendel
- University of North Carolina, Dept. of Genetics, Chapel Hill, NC, USA
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2
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Yeung D, Talukder A, Shi M, Umbach DM, Li Y, Motsinger-Reif A, Fan Z, Li L. Differences in sleep spindle wave density between patients with diabetes mellitus and matched controls: implications for sensing and regulation of peripheral blood glucose. medRxiv 2024:2024.04.11.24305676. [PMID: 38645123 PMCID: PMC11030297 DOI: 10.1101/2024.04.11.24305676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Brain waves during sleep are involved in sensing and regulating peripheral glucose level. Whether brain waves in patients with diabetes differ from those of healthy subjects is unknown. We examined the hypothesis that patients with diabetes have reduced sleep spindle waves, a form of brain wave implicated in periphery glucose regulation during sleep. Methods From a retrospective analysis of polysomnography (PSG) studies on patients who underwent sleep apnea evaluation, we identified 1,214 studies of patients with diabetes mellitus (>66% type 2) and included a sex- and age-matched control subject for each within the scope of our analysis. We similarly identified 376 patients with prediabetes and their matched controls. We extracted spindle characteristics from artifact-removed PSG electroencephalograms and other patient data from records. We used rank-based statistical methods to test hypotheses. We validated our finding on an external PSG dataset. Results Patients with diabetes mellitus exhibited on average about half the spindle density (median=0.38 spindles/min) during sleep as their matched control subjects (median=0.70 spindles/min) (P<2.2e-16). Compared to controls, spindle loss was more pronounced in female patients than in male patients in the frontal regions of the brain (P=0.04). Patients with prediabetes also exhibited signs of lower spindle density compared to matched controls (P=0.01-0.04). Conclusions Patients with diabetes have fewer spindle waves that are implicated in glucose regulation than matched controls during sleep. Besides offering a possible explanation for neurological complications from diabetes, our findings open the possibility that reversing/reducing spindle loss could improve the overall health of patients with diabetes mellitus.
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Affiliation(s)
- Deryck Yeung
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Amlan Talukder
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Min Shi
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - David M. Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Yuanyuan Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Zheng Fan
- Division of Sleep Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Leping Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
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3
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Welch BM, Bommarito PA, Cantonwine DE, Milne GL, Motsinger-Reif A, Edin ML, Zeldin DC, Meeker JD, McElrath TF, Ferguson KK. Predictors of upstream inflammation and oxidative stress pathways during early pregnancy. Free Radic Biol Med 2024; 213:222-232. [PMID: 38262546 PMCID: PMC10922808 DOI: 10.1016/j.freeradbiomed.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Inflammation and oxidative stress are critical to pregnancy, but most human study has focused on downstream, non-causal indicators. Oxylipins are lipid mediators of inflammation and oxidative stress that act through many biological pathways. Our aim was to characterize predictors of circulating oxylipin concentrations based on maternal characteristics. METHODS Our study was conducted among 901 singleton pregnancies in the LIFECODES Fetal Growth Study, a nested case-cohort with recruitment from 2007 to 2018. We measured a targeted panel of oxylipins in early pregnancy plasma and urine samples from several biosynthetic pathways, defined by the polyunsaturated fatty acid (PUFA) precursor and enzyme group. We evaluated levels across predictors, including characteristics of participants' pregnancy, socioeconomic determinants, and obstetric and medical history. RESULTS Current pregnancy and sociodemographic characteristics were the most important predictors of circulating oxylipins concentrations. Plasma oxylipins were lower and urinary oxylipins higher for participants with a later gestational age at sampling (13-23 weeks), higher prepregnancy BMI (obesity class I, II, or III), Black or Hispanic race and ethnicity, and lower socioeconomic status (younger age, lower education, and uninsured). For example, compared to those with normal or underweight prepregnancy BMI, participants with class III prepregnancy obesity had 45-46% lower plasma epoxy-eicosatrienoic acids, the anti-inflammatory oxylipins produced from arachidonic acid (AA) by cytochrome P450, and had 81% higher urinary 15-series F2-isoprostanes, an indicator of oxidative stress produced from non-enzymatic AA oxidation. Similarly, in urine, Black participants had 92% higher prostaglandin E2 metabolite, a pro-inflammatory oxylipin, and 41% higher 5-series F2-isoprostane, an oxidative stress indicator. CONCLUSIONS In this large pregnancy study, we found that circulating levels of oxylipins were different for participants of lower socioeconomic status or of a systematically marginalized racial and ethnic groups. Given associations differed along biosynthetic pathways, results provide insight into etiologic links between maternal predictors and inflammation and oxidative stress.
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Affiliation(s)
- Barrett M Welch
- School of Public Health, University of Nevada, Reno, USA; Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), USA
| | - Paige A Bommarito
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), USA
| | - David E Cantonwine
- Division of Maternal-Fetal Medicine, Brigham and Women's Hospital, Harvard Medical School, USA
| | - Ginger L Milne
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, USA
| | - Matthew L Edin
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, USA
| | - Darryl C Zeldin
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, USA
| | - John D Meeker
- Department of Environmental Health Sciences, University of Michigan School of Public Health, USA
| | - Thomas F McElrath
- Division of Maternal-Fetal Medicine, Brigham and Women's Hospital, Harvard Medical School, USA
| | - Kelly K Ferguson
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), USA.
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4
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Chung MK, House JS, Akhtari FS, Makris KC, Langston MA, Islam KT, Holmes P, Chadeau-Hyam M, Smirnov AI, Du X, Thessen AE, Cui Y, Zhang K, Manrai AK, Motsinger-Reif A, Patel CJ. Decoding the exposome: data science methodologies and implications in exposome-wide association studies (ExWASs). Exposome 2024; 4:osae001. [PMID: 38344436 PMCID: PMC10857773 DOI: 10.1093/exposome/osae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 03/07/2024]
Abstract
This paper explores the exposome concept and its role in elucidating the interplay between environmental exposures and human health. We introduce two key concepts critical for exposomics research. Firstly, we discuss the joint impact of genetics and environment on phenotypes, emphasizing the variance attributable to shared and nonshared environmental factors, underscoring the complexity of quantifying the exposome's influence on health outcomes. Secondly, we introduce the importance of advanced data-driven methods in large cohort studies for exposomic measurements. Here, we introduce the exposome-wide association study (ExWAS), an approach designed for systematic discovery of relationships between phenotypes and various exposures, identifying significant associations while controlling for multiple comparisons. We advocate for the standardized use of the term "exposome-wide association study, ExWAS," to facilitate clear communication and literature retrieval in this field. The paper aims to guide future health researchers in understanding and evaluating exposomic studies. Our discussion extends to emerging topics, such as FAIR Data Principles, biobanked healthcare datasets, and the functional exposome, outlining the future directions in exposomic research. This abstract provides a succinct overview of our comprehensive approach to understanding the complex dynamics of the exposome and its significant implications for human health.
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Affiliation(s)
- Ming Kei Chung
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - John S House
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Farida S Akhtari
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Konstantinos C Makris
- Cyprus International Institute for Environmental and Public Health, School of Health Sciences, Cyprus University of Technology, Limassol, Cyprus
| | - Michael A Langston
- Department of Electrical Engineering and Computer Science, University of TN, Knoxville, TN, USA
| | - Khandaker Talat Islam
- Department of Population and Public Health Sciences, Keck School of Medicine of the University of Southern CA, Los Angeles, CA, USA
| | - Philip Holmes
- Department of Physics, Villanova University, Villanova, Philadelphia, USA
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Alex I Smirnov
- Department of Chemistry, NC State University, Raleigh, NC, USA
| | - Xiuxia Du
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of NC at Charlotte, Charlotte, NC, USA
| | - Anne E Thessen
- Department of Biomedical Informatics, University of CO Anschutz Medical Campus, Aurora, CO, USA
| | - Yuxia Cui
- Exposure, Response, and Technology Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Kai Zhang
- Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of NY, Rensselaer, NY, USA
| | - Arjun K Manrai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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5
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Armstrong ND, Srinivasasainagendra V, Ammous F, Assimes TL, Beitelshees AL, Brody J, Cade BE, Ida Chen YD, Chen H, de Vries PS, Floyd JS, Franceschini N, Guo X, Hellwege JN, House JS, Hwu CM, Kardia SLR, Lange EM, Lange LA, McDonough CW, Montasser ME, O’Connell JR, Shuey MM, Sun X, Tanner RM, Wang Z, Zhao W, Carson AP, Edwards TL, Kelly TN, Kenny EE, Kooperberg C, Loos RJF, Morrison AC, Motsinger-Reif A, Psaty BM, Rao DC, Redline S, Rich SS, Rotter JI, Smith JA, Smith AV, Irvin MR, Arnett DK. Whole genome sequence analysis of apparent treatment resistant hypertension status in participants from the Trans-Omics for Precision Medicine program. Front Genet 2023; 14:1278215. [PMID: 38162683 PMCID: PMC10755672 DOI: 10.3389/fgene.2023.1278215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: Apparent treatment-resistant hypertension (aTRH) is characterized by the use of four or more antihypertensive (AHT) classes to achieve blood pressure (BP) control. In the current study, we conducted single-variant and gene-based analyses of aTRH among individuals from 12 Trans-Omics for Precision Medicine cohorts with whole-genome sequencing data. Methods: Cases were defined as individuals treated for hypertension (HTN) taking three different AHT classes, with average systolic BP ≥ 140 or diastolic BP ≥ 90 mmHg, or four or more medications regardless of BP (n = 1,705). A normotensive control group was defined as individuals with BP < 140/90 mmHg (n = 22,079), not on AHT medication. A second control group comprised individuals who were treatment responsive on one AHT medication with BP < 140/ 90 mmHg (n = 5,424). Logistic regression with kinship adjustment using the Scalable and Accurate Implementation of Generalized mixed models (SAIGE) was performed, adjusting for age, sex, and genetic ancestry. We assessed variants using SKAT-O in rare-variant analyses. Single-variant and gene-based tests were conducted in a pooled multi-ethnicity stratum, as well as self-reported ethnic/racial strata (European and African American). Results: One variant in the known HTN locus, KCNK3, was a top finding in the multi-ethnic analysis (p = 8.23E-07) for the normotensive control group [rs12476527, odds ratio (95% confidence interval) = 0.80 (0.74-0.88)]. This variant was replicated in the Vanderbilt University Medical Center's DNA repository data. Aggregate gene-based signals included the genes AGTPBP, MYL4, PDCD4, BBS9, ERG, and IER3. Discussion: Additional work validating these loci in larger, more diverse populations, is warranted to determine whether these regions influence the pathobiology of aTRH.
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Affiliation(s)
- Nicole D. Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Survey Research Center, Institute for Social Research, Ann Arbor, MI, United States
| | - Themistocles L. Assimes
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Amber L. Beitelshees
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jennifer Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - James S. Floyd
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Jacklyn N. Hellwege
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
| | - John S. House
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Ethan M. Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Leslie A. Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Caitrin W. McDonough
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - May E. Montasser
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | - Megan M. Shuey
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Rikki M. Tanner
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Survey Research Center, Institute for Social Research, Ann Arbor, MI, United States
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States
| | - Todd L. Edwards
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Tanika N. Kelly
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago, Chicago, IL, United States
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Dabeeru C. Rao
- Division of Biostatistics, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Stephen S. Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Survey Research Center, Institute for Social Research, Ann Arbor, MI, United States
| | - Albert V. Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Donna K. Arnett
- Office of the Provost, University of South Carolina, Columbia, SC, United States
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6
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Chan LE, Casiraghi E, Putman T, Reese J, Harmon QE, Schaper K, Hedge H, Valentini G, Schmitt C, Motsinger-Reif A, Hall JE, Mungall CJ, Robinson PN, Haendel MA. Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests. medRxiv 2023:2023.07.14.23292679. [PMID: 37502882 PMCID: PMC10371183 DOI: 10.1101/2023.07.14.23292679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Objective Female reproductive disorders (FRDs) are common health conditions that may present with significant symptoms. Diet and environment are potential areas for FRD interventions. We utilized a knowledge graph (KG) method to predict factors associated with common FRDs (e.g., endometriosis, ovarian cyst, and uterine fibroids). Materials and Methods We harmonized survey data from the Personalized Environment and Genes Study on internal and external environmental exposures and health conditions with biomedical ontology content. We merged the harmonized data and ontologies with supplemental nutrient and agricultural chemical data to create a KG. We analyzed the KG by embedding edges and applying a random forest for edge prediction to identify variables potentially associated with FRDs. We also conducted logistic regression analysis for comparison. Results Across 9765 PEGS respondents, the KG analysis resulted in 8535 significant predicted links between FRDs and chemicals, phenotypes, and diseases. Amongst these links, 32 were exact matches when compared with the logistic regression results, including comorbidities, medications, foods, and occupational exposures. Discussion Mechanistic underpinnings of predicted links documented in the literature may support some of our findings. Our KG methods are useful for predicting possible associations in large, survey-based datasets with added information on directionality and magnitude of effect from logistic regression. These results should not be construed as causal, but can support hypothesis generation. Conclusion This investigation enabled the generation of hypotheses on a variety of potential links between FRDs and exposures. Future investigations should prospectively evaluate the variables hypothesized to impact FRDs.
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Affiliation(s)
- Lauren E Chan
- Oregon State University, College of Public Health and Human Sciences, Corvallis, OR, USA
| | - Elena Casiraghi
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tim Putman
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Justin Reese
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Quaker E Harmon
- National Institute of Environmental Health Sciences, Epidemiology Branch, Durham, NC, USA
| | - Kevin Schaper
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Harshad Hedge
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Giorgio Valentini
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy
| | - Charles Schmitt
- National Institute of Environmental Health Sciences, Office of Data Science, Durham, NC, USA
| | - Alison Motsinger-Reif
- National Institute of Environmental Health Sciences, Biostatistics & Computational Biology Branch, Durham, NC, USA
| | - Janet E Hall
- National Institute of Environmental Health Sciences, Clinical Research Branch, Durham, NC, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
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7
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Lowe ME, Akhtari FS, Potter TA, Fargo DC, Schmitt CP, Schurman SH, Eccles KM, Motsinger-Reif A, Hall JE, Messier KP. The skin is no barrier to mixtures: Air pollutant mixtures and reported psoriasis or eczema in the Personalized Environment and Genes Study (PEGS). J Expo Sci Environ Epidemiol 2023; 33:474-481. [PMID: 36460922 PMCID: PMC10234803 DOI: 10.1038/s41370-022-00502-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 06/03/2023]
Abstract
BACKGROUND Autoimmune (AI) diseases appear to be a product of genetic predisposition and environmental triggers. Disruption of the skin barrier causes exacerbation of psoriasis/eczema. Oxidative stress is a mechanistic pathway for pathogenesis of the disease and is also a primary mechanism for the detrimental effects of air pollution. METHODS We evaluated the association between autoimmune skin diseases (psoriasis or eczema) and air pollutant mixtures in 9060 subjects from the Personalized Environment and Genes Study (PEGS) cohort. Pollutant exposure data on six criteria air pollutants are publicly available from the Center for Air, Climate, and Energy Solutions and the Atmospheric Composition Analysis Group. For increased spatial resolution, we included spatially cumulative exposure to volatile organic compounds from sites in the United States Environmental Protection Agency Toxic Release Inventory and the density of major roads within a 5 km radius of a participant's address from the United States Geological Survey. We applied logistic regression with quantile g-computation, adjusting for age, sex, diagnosis with an autoimmune disease in family or self, and smoking history to evaluate the relationship between self-reported diagnosis of an AI skin condition and air pollution mixtures. RESULTS Only one air pollution variable, sulfate, was significant individually (OR = 1.06, p = 3.99E-2); however, the conditional odds ratio for the combined mixture components of PM2.5 (black carbon, sulfate, sea salt, and soil), CO, SO2, benzene, toluene, and ethylbenzene is 1.10 (p-value = 5.4E-3). SIGNIFICANCE While the etiology of autoimmune skin disorders is not clear, this study provides evidence that air pollutants are associated with an increased prevalence of these disorders. The results provide further evidence of potential health impacts of air pollution exposures on life-altering diseases. SIGNIFICANCE AND IMPACT STATEMENT The impact of air pollution on non-pulmonary and cardiovascular diseases is understudied and under-reported. We find that air pollution significantly increased the odds of psoriasis or eczema in our cohort and the magnitude is comparable to the risk associated with smoking exposure. Autoimmune diseases like psoriasis and eczema are likely impacted by air pollution, particularly complex mixtures and our study underscores the importance of quantifying air pollution-associated risks in autoimmune disease.
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Affiliation(s)
- Melissa E Lowe
- National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Durham, USA.
- National Institute of Environmental Health Sciences, Clinical Research Branch, Durham, USA.
| | - Farida S Akhtari
- National Institute of Environmental Health Sciences, Biostatistics and Computational Biology Branch, Durham, USA
| | - Taylor A Potter
- National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Durham, USA
| | - David C Fargo
- National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Durham, USA
| | - Charles P Schmitt
- National Institute of Environmental Health Sciences, Office of Data Science, Durham, USA
| | - Shepherd H Schurman
- National Institute of Environmental Health Sciences, Clinical Research Branch, Durham, USA
- National Institute on Aging, Clinical Research Core, Bethesda, USA
| | - Kristin M Eccles
- National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Durham, USA
| | - Alison Motsinger-Reif
- National Institute of Environmental Health Sciences, Biostatistics and Computational Biology Branch, Durham, USA
| | - Janet E Hall
- National Institute of Environmental Health Sciences, Clinical Research Branch, Durham, USA
| | - Kyle P Messier
- National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Durham, USA
- National Institute of Environmental Health Sciences, Clinical Research Branch, Durham, USA
- National Institute of Environmental Health Sciences, Biostatistics and Computational Biology Branch, Durham, USA
- National Institute on Minority Health and Health Disparities, Bethesda, USA
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8
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Brown E, Shekhar S, Delaney A, Burkholder AB, Plummer L, Mericq V, Merino PM, Quinton R, Lewis KL, Shaw ND, Welt CK, Martin KA, Seminara SB, Biesecker LG, Motsinger-Reif A, House JS, Hall J. LBMON114 Enrichment Of Rare Sequence Variants In Genes That Communicate Metabolic Signals To The GnRH System In Hypothalamic Amenorrhea. J Endocr Soc 2022. [PMCID: PMC9627140 DOI: 10.1210/jendso/bvac150.970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Introduction Functional hypothalamic amenorrhea (HA) is commonly associated with increased exercise or decreased caloric intake and often with stress. We have previously demonstrated an increased burden of rare sequence variants (RSVs) in genes involved in GnRH ontogeny and upstream regulation in women with HA, but the role of metabolic and stress signaling to the GnRH neuronal system is poorly defined in this population. Methods The study included 100 women with a confirmed diagnosis of HA. The control cohort consisted of 468 women (aged 45-65 years) drawn from the NIH ClinSeq® Project. Exome sequencing was performed on peripheral blood genomic DNA. A subset of 72 genes was analyzed that have been shown to: 1) link metabolic or stress with reproductive phenotypes or 2) integrate metabolic and stress pathways with control of GnRH secretion. Joint genotyping of case and control samples was performed using the GATK GenotypeGVCFs function, locus-filtering using the VariantRecalibrator function, and genotype refinement using CalculateGenotypePosteriors with computation of median depths. Median depth positions <10, positions failing GATK VQSR or GATK genotype quality scores <20 were excluded. RSVs were identified by < 1% frequency in any subpopulation in gnomeAD for all-subjects (AS) and < 1% frequency in non-Finnish Europeans for Caucasians (CS). Data were analyzed for AS and for CS using a one-sided Fisher exact test for metabolism genes and stress genes. An additional regression analysis was conducted on the number of RSVs in a given gene as a predictor of HA vs. control. Comparisons with a p-value of < 0.1 are reported. Results HA patients exhibited an increased burden of RSVs in metabolism genes vs. controls (AS p=0. 043; CS p=0.105). The total number of RSVs per gene highlighted differences between HA and controls for the following genes: ADAMTSL1, GRINA, GRIN1, HCRTR1, TENM3, and NOS1 (AS p<0. 001, p=0. 032, p=0. 057, p=0. 082, p=0. 091, p=0. 095; CS p=0. 024, p=0. 044, p=0. 044, p NS, p=0. 086, p NS). Interestingly, RSVs in NOS1 and TENM3 appeared to be protective for HA (odds ratio <1 for both). In contrast, candidate stress genes were not significant in either the AS or CS (p=0.788, p=0.910). Conclusions These data suggest that RSVs in genes involved in phenotypes or signaling pathways that link metabolism to GnRH secretion may predispose to development of HA in the setting of decreased energy balance, but not for stress-related genes. GRINA and GRIN1 are important components of glutamate signaling that facilitate both appetite and GnRH secretion either directly or through kisspeptin. HCRTR1 plays a similar role in linking appetite and GnRH secretion while NOS1, which facilitates kisspeptin signaling, may be protective. This work highlights the need for further studies to understand the potential roles of ADAMTSL1 and TENM3 as risk factors for HA. Presentation: Monday, June 13, 2022 12:30 p.m. - 2:30 p.m.
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9
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Lewis AM, Thomas R, Breen M, Peden K, Teferedegne B, Foseh G, Motsinger-Reif A, Rotroff D, Lewis G. The AGMK1-9T7 cell model of neoplasia: Evolution of DNA copy-number aberrations and miRNA expression during transition from normal to metastatic cancer cells. PLoS One 2022; 17:e0275394. [PMID: 36279283 PMCID: PMC9591059 DOI: 10.1371/journal.pone.0275394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/15/2022] [Indexed: 01/24/2023] Open
Abstract
To study neoplasia in tissue culture, cell lines representing the evolution of normal cells to tumor cells are needed. To produce such cells, we developed the AGMK1-9T7 cell line, established cell banks at 10-passage intervals, and characterized their biological properties. Here we examine the evolution of chromosomal DNA copy-number aberrations and miRNA expression in this cell line from passage 1 to the acquisition of a tumorigenic phenotype at passage 40. We demonstrated the use of a human microarray platform for DNA copy-number profiling of AGMK1-9T7 cells using knowledge of synteny to 'recode' data from human chromosome coordinates to those of the African green monkey. This approach revealed the accumulation of DNA copy-number gains and losses in AGMK1-9T7 cells from passage 3 to passage 40, which spans the period in which neoplastic transformation occurred. These alterations occurred in the sequences of genes regulating DNA copy-number imbalance of several genes that regulate endothelial cell angiogenesis, survival, migration, and proliferation. Regarding miRNA expression, 195 miRNAs were up- or down-regulated at passage 1 at levels that appear to be biologically relevant (i.e., log2 fold change >2.0 (q<0.05)). At passage 10, the number of up/down-regulated miRNAs fell to 63; this number increased to 93 at passage 40. Principal-component analysis grouped these miRNAs into 3 clusters; miRNAs in sub-clusters of these groups could be correlated with initiation, promotion, and progression, stages that have been described for neoplastic development. Thirty-four of the AGMK1-9T7 miRNAs have been associated with these stages in human cancer. Based on these data, we propose that the evolution of AGMK1-9T7 cells represents a detailed model of neoplasia in vitro.
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Affiliation(s)
- Andrew M. Lewis
- Laboratory of DNA Viruses, Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States of America
- * E-mail:
| | - Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, and Center for Comparative Medicine and Translational Research, Raleigh, NC, United States of America
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, and Center for Comparative Medicine and Translational Research, Raleigh, NC, United States of America
| | - Keith Peden
- Laboratory of DNA Viruses, Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States of America
| | - Belete Teferedegne
- Laboratory of DNA Viruses, Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States of America
| | - Gideon Foseh
- Laboratory of DNA Viruses, Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States of America
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh NC, United States of America
| | - Daniel Rotroff
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh NC, United States of America
| | - Gladys Lewis
- TCL and M Associates, Leesburg, VA, United States of America
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10
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Mandal M, Levy J, Ives C, Hwang S, Zhou YH, Motsinger-Reif A, Pan H, Huggins W, Hamilton C, Wright F, Edwards S. Correlation Analysis of Variables From the Atherosclerosis Risk in Communities Study. Front Pharmacol 2022; 13:883433. [PMID: 35899108 PMCID: PMC9310100 DOI: 10.3389/fphar.2022.883433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
The need to test chemicals in a timely and cost-effective manner has driven the development of new alternative methods (NAMs) that utilize in silico and in vitro approaches for toxicity prediction. There is a wealth of existing data from human studies that can aid in understanding the ability of NAMs to support chemical safety assessment. This study aims to streamline the integration of data from existing human cohorts by programmatically identifying related variables within each study. Study variables from the Atherosclerosis Risk in Communities (ARIC) study were clustered based on their correlation within the study. The quality of the clusters was evaluated via a combination of manual review and natural language processing (NLP). We identified 391 clusters including 3,285 variables. Manual review of the clusters containing more than one variable determined that human reviewers considered 95% of the clusters related to some degree. To evaluate potential bias in the human reviewers, clusters were also scored via NLP, which showed a high concordance with the human classification. Clusters were further consolidated into cluster groups using the Louvain community finding algorithm. Manual review of the cluster groups confirmed that clusters within a group were more related than clusters from different groups. Our data-driven approach can facilitate data harmonization and curation efforts by providing human annotators with groups of related variables reflecting the themes present in the data. Reviewing groups of related variables should increase efficiency of the human review, and the number of variables reviewed can be reduced by focusing curator attention on variable groups whose theme is relevant for the topic being studied.
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Affiliation(s)
- Meisha Mandal
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Josh Levy
- Levy Informatics, Chapel Hill, NC, United States
| | - Cataia Ives
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Stephen Hwang
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Yi-Hui Zhou
- Department of Statistics, North Carolina State University, Raleigh, NC, United States
- Bioinformatics Research Center and Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Huaqin Pan
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Wayne Huggins
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Carol Hamilton
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Fred Wright
- Department of Statistics, North Carolina State University, Raleigh, NC, United States
- Bioinformatics Research Center and Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Stephen Edwards
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
- *Correspondence: Stephen Edwards,
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11
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Jima DD, Skaar DA, Planchart A, Motsinger-Reif A, Cevik SE, Park SS, Cowley M, Wright F, House J, Liu A, Jirtle RL, Hoyo C. Genomic map of candidate human imprint control regions: the imprintome. Epigenetics 2022; 17:1920-1943. [PMID: 35786392 PMCID: PMC9665137 DOI: 10.1080/15592294.2022.2091815] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Imprinted genes – critical for growth, metabolism, and neuronal function – are expressed from one parental allele. Parent-of-origin-dependent CpG methylation regulates this expression at imprint control regions (ICRs). Since ICRs are established before tissue specification, these methylation marks are similar across cell types. Thus, they are attractive for investigating the developmental origins of adult diseases using accessible tissues, but remain unknown. We determined genome-wide candidate ICRs in humans by performing whole-genome bisulphite sequencing (WGBS) of DNA derived from the three germ layers and from gametes. We identified 1,488 hemi-methylated candidate ICRs, including 19 of 25 previously characterized ICRs (https://humanicr.org/). Gamete methylation approached 0% or 100% in 332 ICRs (178 paternally and 154 maternally methylated), supporting parent-of-origin-specific methylation, and 65% were in well-described CTCF-binding or DNaseI hypersensitive regions. This draft of the human imprintome will allow for the systematic determination of the role of early-acquired imprinting dysregulation in the pathogenesis of human diseases and developmental and behavioural disorders.
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Affiliation(s)
- Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - David A Skaar
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Antonio Planchart
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Sebnem E Cevik
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Sarah S Park
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.,Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Michael Cowley
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Fred Wright
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - John House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Andy Liu
- Department of Neurology, Duke University, School of Medicine, Durham, NC, USA
| | - Randy L Jirtle
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
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12
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Wolkin A, Collier S, House JS, Reif D, Motsinger-Reif A, Duca L, Sharpe JD. Comparison of National Vulnerability Indices Used by the Centers for Disease Control and Prevention for the COVID-19 Response. Public Health Rep 2022; 137:803-812. [PMID: 35514159 PMCID: PMC9257512 DOI: 10.1177/00333549221090262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Vulnerability indices use quantitative indicators and geospatial data to examine the level of vulnerability to morbidity in a community. The Centers for Disease Control and Prevention (CDC) uses 3 indices for the COVID-19 response: the CDC Social Vulnerability Index (CDC-SVI), the US COVID-19 Community Vulnerability Index (CCVI), and the Pandemic Vulnerability Index (PVI). The objective of this review was to describe these tools and explain the similarities and differences between them. METHODS We described the 3 indices, outlined the underlying data sources and metrics for each, and discussed their use by CDC for the COVID-19 response. We compared the percentile score for each county for each index by calculating Spearman correlation coefficients (Spearman ρ). RESULTS These indices have some, but not all, component metrics in common. The CDC-SVI is a validated metric that estimates social vulnerability, which comprises the underlying population-level characteristics that influence differences in health risk among communities. To address risk specific to the COVID-19 pandemic, the CCVI and PVI build on the CDC-SVI and include additional variables. The 3 indices were highly correlated. Spearman ρ for comparisons between the CDC-SVI score and the CCVI and between the CCVI and the PVI score was 0.83. Spearman ρ for the comparison between the CDC-SVI score and PVI score was 0.73. CONCLUSION The indices can empower local and state public health officials with additional information to focus resources and interventions on disproportionately affected populations to combat the ongoing pandemic and plan for future pandemics.
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Affiliation(s)
- Amy Wolkin
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sarah Collier
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John S. House
- Biostatistics and Computational Biology Branch, National Institute for Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - David Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute for Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Lindsey Duca
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - J. Danielle Sharpe
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, GA, USA
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13
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Miller MF, Shi M, Motsinger-Reif A, Weinberg CR, Miller JD, Nichols E. Community-Based Testing Sites for SARS-CoV-2 - United States, March 2020-November 2021. MMWR Morb Mortal Wkly Rep 2021; 70:1706-1711. [PMID: 34882655 PMCID: PMC8659188 DOI: 10.15585/mmwr.mm7049a3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Abstract
Background Cancer is one of the main causes of death worldwide. Combination drug therapy has been a mainstay of cancer treatment for decades and has been shown to reduce host toxicity and prevent the development of acquired drug resistance. However, the immense number of possible drug combinations and large synergistic space makes it infeasible to screen all effective drug pairs experimentally. Therefore, it is crucial to develop computational approaches to predict drug synergy and guide experimental design for the discovery of rational combinations for therapy. Results We present a new deep learning approach to predict synergistic drug combinations by integrating gene expression profiles from cell lines and chemical structure data. Specifically, we use principal component analysis (PCA) to reduce the dimensionality of the chemical descriptor data and gene expression data. We then propagate the low-dimensional data through a neural network to predict drug synergy values. We apply our method to O’Neil’s high-throughput drug combination screening data as well as a dataset from the AstraZeneca-Sanger Drug Combination Prediction DREAM Challenge. We compare the neural network approach with and without dimension reduction. Additionally, we demonstrate the effectiveness of our deep learning approach and compare its performance with three state-of-the-art machine learning methods: Random Forests, XGBoost, and elastic net, with and without PCA-based dimensionality reduction. Conclusions Our developed approach outperforms other machine learning methods, and the use of dimension reduction dramatically decreases the computation time without sacrificing accuracy.
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Affiliation(s)
- Jun Ma
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Drive, Durham, NC, 27709, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Drive, Durham, NC, 27709, USA.
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15
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Green AJ, Anchang B, Akhtari FS, Reif DM, Motsinger-Reif A. Extending the lymphoblastoid cell line model for drug combination pharmacogenomics. Pharmacogenomics 2021; 22:543-551. [PMID: 34044623 DOI: 10.2217/pgs-2020-0160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Combination drug therapies have become an integral part of precision oncology, and while evidence of clinical effectiveness continues to grow, the underlying mechanisms supporting synergy are poorly understood. Immortalized human lymphoblastoid cell lines (LCLs) have been proven as a particularly useful, scalable and low-cost model in pharmacogenetics research, and are suitable for elucidating the molecular mechanisms of synergistic combination therapies. In this review, we cover the advantages of LCLs in synergy pharmacogenomics and consider recent studies providing initial evidence of the utility of LCLs in synergy research. We also discuss several opportunities for LCL-based systems to address gaps in the research through the expansion of testing regimens, assessment of new drug classes and higher-order combinations, and utilization of integrated omics technologies.
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Affiliation(s)
- Adrian J Green
- Department of Biological Sciences & the Bioinformatics Research Center, NC State University, Raleigh, NC, USA
| | - Benedict Anchang
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Farida S Akhtari
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - David M Reif
- Department of Biological Sciences & the Bioinformatics Research Center, NC State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
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16
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Sikdar S, Wyss AB, Lee MK, Hoang TT, Richards M, Beane Freeman LE, Parks C, Thorne PS, Hankinson JL, Umbach DM, Motsinger-Reif A, London SJ. Interaction between Genetic Risk Scores for reduced pulmonary function and smoking, asthma and endotoxin. Thorax 2021; 76:1219-1226. [PMID: 33963087 PMCID: PMC8572320 DOI: 10.1136/thoraxjnl-2020-215624] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 02/17/2021] [Accepted: 03/22/2021] [Indexed: 01/04/2023]
Abstract
Rationale Genome-wide association studies (GWASs) have identified numerous loci associated with lower pulmonary function. Pulmonary function is strongly related to smoking and has also been associated with asthma and dust endotoxin. At the individual SNP level, genome-wide analyses of pulmonary function have not identified appreciable evidence for gene by environment interactions. Genetic Risk Scores (GRSs) may enhance power to identify gene–environment interactions, but studies are few. Methods We analysed 2844 individuals of European ancestry with 1000 Genomes imputed GWAS data from a case–control study of adult asthma nested within a US agricultural cohort. Pulmonary function traits were FEV1, FVC and FEV1/FVC. Using data from a recent large meta-analysis of GWAS, we constructed a weighted GRS for each trait by combining the top (p value<5×10−9) genetic variants, after clumping based on distance (±250 kb) and linkage disequilibrium (r2=0.5). We used linear regression, adjusting for relevant covariates, to estimate associations of each trait with its GRS and to assess interactions. Results Each trait was highly significantly associated with its GRS (all three p values<8.9×10−8). The inverse association of the GRS with FEV1/FVC was stronger for current smokers (pinteraction=0.017) or former smokers (pinteraction=0.064) when compared with never smokers and among asthmatics compared with non-asthmatics (pinteraction=0.053). No significant interactions were observed between any GRS and house dust endotoxin. Conclusions Evaluation of interactions using GRSs supports a greater impact of increased genetic susceptibility on reduced pulmonary function in the presence of smoking or asthma.
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Affiliation(s)
- Sinjini Sikdar
- Department of Mathematics and Statistics, Old Dominion University, Norfolk, Virginia, USA.,Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Thanh T Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | | | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Christine Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Peter S Thorne
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa, USA
| | | | - David M Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
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17
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Marvel SW, House JS, Wheeler M, Song K, Zhou YH, Wright FA, Chiu WA, Rusyn I, Motsinger-Reif A, Reif DM. The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring County-Level Vulnerability Using Visualization, Statistical Modeling, and Machine Learning. Environ Health Perspect 2021; 129:17701. [PMID: 33400596 PMCID: PMC7785295 DOI: 10.1289/ehp8690] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 05/10/2023]
Affiliation(s)
- Skylar W. Marvel
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA
| | - John S. House
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Matthew Wheeler
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Kuncheng Song
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA
| | - Yi-Hui Zhou
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA
| | - Fred A. Wright
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA
- Department of Statistics, NCSU, Raleigh, North Carolina, USA
| | - Weihsueh A. Chiu
- Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Ivan Rusyn
- Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - David M. Reif
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA
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18
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Marvel SW, House JS, Wheeler M, Song K, Zhou Y, Wright FA, Chiu WA, Rusyn I, Motsinger-Reif A, Reif DM. The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring county-level vulnerability using visualization, statistical modeling, and machine learning. medRxiv 2020:2020.08.10.20169649. [PMID: 32817964 PMCID: PMC7430608 DOI: 10.1101/2020.08.10.20169649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND While the COVID-19 pandemic presents a global challenge, the U.S. response places substantial responsibility for both decision-making and communication on local health authorities, necessitating tools to support decision-making at the community level. OBJECTIVES We created a Pandemic Vulnerability Index (PVI) to support counties and municipalities by integrating baseline data on relevant community vulnerabilities with dynamic data on local infection rates and interventions. The PVI visually synthesizes county-level vulnerability indicators, enabling their comparison in regional, state, and nationwide contexts. METHODS We describe the data streams used and how these are combined to calculate the PVI, detail the supporting epidemiological modeling and machine-learning forecasts, and outline the deployment of an interactive web Dashboard. Finally, we describe the practical application of the PVI for real-world decision-making. RESULTS Considering an outlook horizon from 1 to 28 days, the overall PVI scores are significantly associated with key vulnerability-related outcome metrics of cumulative deaths, population adjusted cumulative deaths, and the proportion of deaths from cases. The modeling results indicate the most significant predictors of case counts are population size, proportion of black residents, and mean PM2.5. The machine learning forecast results were strongly predictive of observed cases and deaths up to 14 days ahead. The modeling reinforces an integrated concept of vulnerability that accounts for both dynamic and static data streams and highlights the drivers of inequities in COVID-19 cases and deaths. These results also indicate that local areas with a highly ranked PVI should take near-term action to mitigate vulnerability. DISCUSSION The COVID-19 PVI Dashboard monitors multiple data streams to communicate county-level trends and vulnerabilities and facilitates decision-making and communication among government officials, scientists, community leaders, and the public to enable effective and coordinated action to combat the pandemic.
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Affiliation(s)
- Skylar W. Marvel
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - John S. House
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Matthew Wheeler
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Kuncheng Song
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Yihui Zhou
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Fred A. Wright
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA
| | - Weihsueh A. Chiu
- Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845, USA
| | - Ivan Rusyn
- Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - David M. Reif
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
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19
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Hoang TT, Sikdar S, Xu CJ, Lee MK, Cardwell J, Forno E, Imboden M, Jeong A, Madore AM, Qi C, Wang T, Bennett BD, Ward JM, Parks CG, Beane-Freeman LE, King D, Motsinger-Reif A, Umbach DM, Wyss AB, Schwartz DA, Celedón JC, Laprise C, Ober C, Probst-Hensch N, Yang IV, Koppelman GH, London SJ. Epigenome-wide association study of DNA methylation and adult asthma in the Agricultural Lung Health Study. Eur Respir J 2020; 56:13993003.00217-2020. [PMID: 32381493 PMCID: PMC7469973 DOI: 10.1183/13993003.00217-2020] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/15/2020] [Indexed: 12/11/2022]
Abstract
Epigenome-wide studies of methylation in children support a role for epigenetic mechanisms in asthma; however, studies in adults are rare and few have examined non-atopic asthma. We conducted the largest epigenome-wide association study (EWAS) of blood DNA methylation in adults in relation to non-atopic and atopic asthma. We measured DNA methylation in blood using the Illumina MethylationEPIC array among 2286 participants in a case-control study of current adult asthma nested within a United States agricultural cohort. Atopy was defined by serum specific immunoglobulin E (IgE). Participants were categorised as atopy without asthma (n=185), non-atopic asthma (n=673), atopic asthma (n=271), or a reference group of neither atopy nor asthma (n=1157). Analyses were conducted using logistic regression. No associations were observed with atopy without asthma. Numerous cytosine–phosphate–guanine (CpG) sites were differentially methylated in non-atopic asthma (eight at family-wise error rate (FWER) p<9×10−8, 524 at false discovery rate (FDR) less than 0.05) and implicated 382 novel genes. More CpG sites were identified in atopic asthma (181 at FWER, 1086 at FDR) and implicated 569 novel genes. 104 FDR CpG sites overlapped. 35% of CpG sites in non-atopic asthma and 91% in atopic asthma replicated in studies of whole blood, eosinophils, airway epithelium, or nasal epithelium. Implicated genes were enriched in pathways related to the nervous system or inflammation. We identified numerous, distinct differentially methylated CpG sites in non-atopic and atopic asthma. Many CpG sites from blood replicated in asthma-relevant tissues. These circulating biomarkers reflect risk and sequelae of disease, as well as implicate novel genes associated with non-atopic and atopic asthma. Distinct methylation signals are found in non-atopic and atopic asthma. Most are related to gene expression and are replicated in asthma-relevant tissues, confirming the value of blood DNA methylation for identifying novel genes linked in asthma pathogenesis.https://bit.ly/2VnbJg3
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Affiliation(s)
- Thanh T Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA.,Joint first authors
| | - Sinjini Sikdar
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA.,Dept of Mathematics and Statistics, Old Dominion University, Norfolk, VA, USA.,Joint first authors
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Centre for Experimental and Clinical Infection Research (TWINCORE), Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Joint first authors
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Jonathan Cardwell
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Erick Forno
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.,Dept of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Medea Imboden
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Dept of Public Health, University of Basel, Basel, Switzerland
| | - Ayoung Jeong
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Dept of Public Health, University of Basel, Basel, Switzerland
| | - Anne-Marie Madore
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Cancan Qi
- Dept of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital and GRIAC Research Institute, Groningen, The Netherlands
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Brian D Bennett
- Integrative Bioinformatics Support Group, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - James M Ward
- Integrative Bioinformatics Support Group, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Christine G Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Laura E Beane-Freeman
- Occupational and Environmental Epidemiology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Debra King
- Clinical Pathology Group, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - David M Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - David A Schwartz
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Juan C Celedón
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.,Dept of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada.,Centre Intersectoriel en Santé Durable, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada.,Dept of Pediatrics, Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean, Saguenay, QC, Canada
| | - Carole Ober
- Dept of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Nicole Probst-Hensch
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Dept of Public Health, University of Basel, Basel, Switzerland
| | - Ivana V Yang
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gerard H Koppelman
- Dept of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital and GRIAC Research Institute, Groningen, The Netherlands
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
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20
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Wise CF, Hammel SC, Herkert N, Ma J, Motsinger-Reif A, Stapleton HM, Breen M. Comparative Exposure Assessment Using Silicone Passive Samplers Indicates That Domestic Dogs Are Sentinels To Support Human Health Research. Environ Sci Technol 2020; 54:7409-7419. [PMID: 32401030 PMCID: PMC7655112 DOI: 10.1021/acs.est.9b06605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Silicone wristbands are promising passive samplers to support epidemiological studies in characterizing exposure to organic contaminants; however, investigating associated health risks remains challenging because of the latency period for many chronic diseases that take years to manifest. Dogs provide valuable insights as sentinels for exposure-related human disease because they share similar exposures in the home, have shorter life spans, share many clinical/biological features, and have closely related genomes. Here, we evaluated exposures among pet dogs and their owners using silicone dog tags and wristbands to determine if contaminant levels were correlated with validated exposure biomarkers. Significant correlations between measures on dog tags and wristbands were observed (rs = 0.38-0.90; p < 0.05). Correlations with their respective urinary biomarkers were stronger in dog tags compared to that in human wristbands (rs = 0.50-0.71; p < 0.01) for several organophosphate esters. This supports the value of using silicone bands with dogs to investigate health impacts on humans from shared exposures.
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Affiliation(s)
- Catherine F. Wise
- Department of Biological Sciences, Environmental and Molecular Toxicology Program, North Carolina State University, 850 Main Campus Drive, Raleigh, North Carolina 27606, United States
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, North Carolina 27607, United States
| | - Stephanie C. Hammel
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas Herkert
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27708, United States
| | - Jun Ma
- Department of Statistics, North Carolina State University, Raleigh, North Carolina 27607, United States
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina 27709, United States
| | - Heather M. Stapleton
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27708, United States
- Duke Cancer Institute, Durham, North Carolina, United States
| | - Matthew Breen
- Department of Biological Sciences, Environmental and Molecular Toxicology Program, North Carolina State University, 850 Main Campus Drive, Raleigh, North Carolina 27606, United States
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, North Carolina 27607, United States
- Duke Cancer Institute, Durham, North Carolina, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27607, United States
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27607, United States
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21
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Ma J, Bair E, Motsinger-Reif A. Nonlinear Dose-Response Modeling of High-Throughput Screening Data Using an Evolutionary Algorithm. Dose Response 2020; 18:1559325820926734. [PMID: 32547333 PMCID: PMC7249578 DOI: 10.1177/1559325820926734] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/13/2020] [Accepted: 04/17/2020] [Indexed: 11/17/2022] Open
Abstract
Nonlinear dose-response relationships exist extensively in the cellular, biochemical, and physiologic processes that are affected by varying levels of biological, chemical, or radiation stress. Modeling such responses is a crucial component of toxicity testing and chemical screening. Traditional model fitting methods such as nonlinear least squares (NLS) are very sensitive to initial parameter values and often had convergence failure. The use of evolutionary algorithms (EAs) has been proposed to address many of the limitations of traditional approaches, but previous methods have been limited in the types of models they can fit. Therefore, we propose the use of an EA for dose-response modeling for a range of potential response model functional forms. This new method can not only fit the most commonly used nonlinear dose-response models (eg, exponential models and 3-, 4-, and 5-parameter logistic models) but also select the best model if no model assumption is made, which is especially useful in the case of high-throughput curve fitting. Compared with NLS, the new method provides stable and robust solutions without sensitivity to initial values.
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Affiliation(s)
- Jun Ma
- Bioinformatics Research Center, North Carolina State University, Durham, NC, USA.,Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | | | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
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22
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Crestani E, Harb H, Charbonnier LM, Leirer J, Motsinger-Reif A, Rachid R, Phipatanakul W, Kaddurah-Daouk R, Chatila TA. Untargeted metabolomic profiling identifies disease-specific signatures in food allergy and asthma. J Allergy Clin Immunol 2020; 145:897-906. [PMID: 31669435 PMCID: PMC7062570 DOI: 10.1016/j.jaci.2019.10.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/10/2019] [Accepted: 10/01/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Food allergy (FA) affects an increasing proportion of children for reasons that remain obscure. Novel disease biomarkers and curative treatment options are strongly needed. OBJECTIVE We sought to apply untargeted metabolomic profiling to identify pathogenic mechanisms and candidate disease biomarkers in patients with FA. METHODS Mass spectrometry-based untargeted metabolomic profiling was performed on serum samples of children with either FA alone, asthma alone, or both FA and asthma, as well as healthy pediatric control subjects. RESULTS In this pilot study patients with FA exhibited a disease-specific metabolomic signature compared with both control subjects and asthmatic patients. In particular, FA was uniquely associated with a marked decrease in sphingolipid levels, as well as levels of a number of other lipid metabolites, in the face of normal frequencies of circulating natural killer T cells. Specific comparison of patients with FA and asthmatic patients revealed differences in the microbiota-sensitive aromatic amino acid and secondary bile acid metabolism. Children with both FA and asthma exhibited a metabolomic profile that aligned with that of FA alone but not asthma. Among children with FA, the history of severe systemic reactions and the presence of multiple FAs were associated with changes in levels of tryptophan metabolites, eicosanoids, plasmalogens, and fatty acids. CONCLUSIONS Children with FA have a disease-specific metabolomic profile that is informative of disease mechanisms and severity and that dominates in the presence of asthma. Lower levels of sphingolipids and ceramides and other metabolomic alterations observed in children with FA might reflect the interplay between an altered microbiota and immune cell subsets in the gut.
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Affiliation(s)
- Elena Crestani
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Hani Harb
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Louis-Marie Charbonnier
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Jonathan Leirer
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - Rima Rachid
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Wanda Phipatanakul
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences and the Duke Institute for Brain Sciences, Duke University, Durham, NC
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass.
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23
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Sikdar S, Joehanes R, Joubert BR, Xu CJ, Vives-Usano M, Rezwan FI, Felix JF, Ward JM, Guan W, Richmond RC, Brody JA, Küpers LK, Baïz N, Håberg SE, Smith JA, Reese SE, Aslibekyan S, Hoyo C, Dhingra R, Markunas CA, Xu T, Reynolds LM, Just AC, Mandaviya PR, Ghantous A, Bennett BD, Wang T, Consortium TBIOS, Bakulski KM, Melen E, Zhao S, Jin J, Herceg Z, van Meurs J, Taylor JA, Baccarelli AA, Murphy SK, Liu Y, Munthe-Kaas MC, Deary IJ, Nystad W, Waldenberger M, Annesi-Maesano I, Conneely K, Jaddoe VWV, Arnett D, Snieder H, Kardia SLR, Relton CL, Ong KK, Ewart S, Moreno-Macias H, Romieu I, Sotoodehnia N, Fornage M, Motsinger-Reif A, Koppelman GH, Bustamante M, Levy D, London SJ. Comparison of smoking-related DNA methylation between newborns from prenatal exposure and adults from personal smoking. Epigenomics 2019; 11:1487-1500. [PMID: 31536415 PMCID: PMC6836223 DOI: 10.2217/epi-2019-0066] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/13/2019] [Indexed: 12/17/2022] Open
Abstract
Aim: Cigarette smoking influences DNA methylation genome wide, in newborns from pregnancy exposure and in adults from personal smoking. Whether a unique methylation signature exists for in utero exposure in newborns is unknown. Materials & methods: We separately meta-analyzed newborn blood DNA methylation (assessed using Illumina450k Beadchip), in relation to sustained maternal smoking during pregnancy (9 cohorts, 5648 newborns, 897 exposed) and adult blood methylation and personal smoking (16 cohorts, 15907 participants, 2433 current smokers). Results & conclusion: Comparing meta-analyses, we identified numerous signatures specific to newborns along with many shared between newborns and adults. Unique smoking-associated genes in newborns were enriched in xenobiotic metabolism pathways. Our findings may provide insights into specific health impacts of prenatal exposure on offspring.
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Affiliation(s)
- Sinjini Sikdar
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Roby Joehanes
- Hebrew SeniorLife, Harvard Medical School, Boston, MA 02115, USA
- Framingham Heart Study, Framingham, MA 01702, USA
| | - Bonnie R Joubert
- Department of Health & Human Services, Division of Extramural Research & Training, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Cheng-Jian Xu
- Department of Pediatric Pulmonology & Pediatric Allergology, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
| | - Marta Vives-Usano
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Center for Genomic Regulation (CRG), Barcelona Institute of Science & Technology, Barcelona, Spain
| | - Faisal I Rezwan
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Janine F Felix
- The Generation R Study Group, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - James M Ward
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | - Jennifer A Brody
- Department of Medicine, Epidemiology, & Health Services, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98101, USA
| | - Leanne K Küpers
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Division of Human Nutrition & Health, Wageningen University, Wageningen, The Netherlands
| | - Nour Baïz
- Epidemiology of Allergic & Respiratory Diseases Department (EPAR), Sorbonne Universités, INSERM, Pierre Louis Institute of Epidemiology & Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Siri E Håberg
- Centre for Fertility & Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah E Reese
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Stella Aslibekyan
- College of Public Health, University of Kentucky, Lexington, KY 40536, USA
| | - Cathrine Hoyo
- Department of Biological Sciences & Center for Human Health & the Environment, North Carolina State University, Raleigh, NC 27695, USA
| | - Radhika Dhingra
- Department of Environmental Sciences & Engineering, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Christina A Markunas
- Behavioral Health Research Division, RTI International, Research Triangle Park, NC 27709, USA
| | - Tao Xu
- Research Unit of Molecular Epidemiology, Helmhotz Zentrum Muenchen, Munich, Germany
| | - Lindsay M Reynolds
- Department of Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Allan C Just
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Pooja R Mandaviya
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Brian D Bennett
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Tianyuan Wang
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - The BIOS Consortium
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- Hebrew SeniorLife, Harvard Medical School, Boston, MA 02115, USA
- Framingham Heart Study, Framingham, MA 01702, USA
- Department of Health & Human Services, Division of Extramural Research & Training, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- Department of Pediatric Pulmonology & Pediatric Allergology, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Center for Genomic Regulation (CRG), Barcelona Institute of Science & Technology, Barcelona, Spain
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
- The Generation R Study Group, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
- Department of Medicine, Epidemiology, & Health Services, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98101, USA
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Division of Human Nutrition & Health, Wageningen University, Wageningen, The Netherlands
- Epidemiology of Allergic & Respiratory Diseases Department (EPAR), Sorbonne Universités, INSERM, Pierre Louis Institute of Epidemiology & Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
- Centre for Fertility & Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- College of Public Health, University of Kentucky, Lexington, KY 40536, USA
- Department of Biological Sciences & Center for Human Health & the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Department of Environmental Sciences & Engineering, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC 27599, USA
- Behavioral Health Research Division, RTI International, Research Triangle Park, NC 27709, USA
- Research Unit of Molecular Epidemiology, Helmhotz Zentrum Muenchen, Munich, Germany
- Department of Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Westat, Durham, NC 27703, USA
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York City, NY 10032, USA
- Departments of Obstetrics & Gynecology & Pathology, Duke University School of Medicine, Durham, NC 27708, USA
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway
- National Institute of Public Health, Oslo, Norway
- Centre for Cognitive Ageing & Cognitive Epidemiology, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
- Division of Mental & Physical Health, Norwegian Institute of Public Health, Oslo, Norway
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
- Autonomous Metropolitan University Iztapalapa, Mexico City, Mexico
- Nutrition & Metabolism Section, International Agency for Research on Cancer, Lyon, France
- Center for Research on Population Health, National Institute of Public Health, Mexico
- Hubert Department of Global Health, Emory University, Atlanta, GA 30329, USA
- Institute of Molecular Medicine & Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
- Population Sciences Branch, National Heart, Lung, & Blood Institute, National Institutes of Health, Bethesda, MD 01702, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erik Melen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shanshan Zhao
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | | | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jack A Taylor
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York City, NY 10032, USA
| | - Susan K Murphy
- Departments of Obstetrics & Gynecology & Pathology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Monica Cheng Munthe-Kaas
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway
- National Institute of Public Health, Oslo, Norway
| | - Ian J Deary
- Centre for Cognitive Ageing & Cognitive Epidemiology, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Wenche Nystad
- Division of Mental & Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmhotz Zentrum Muenchen, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Isabella Annesi-Maesano
- Epidemiology of Allergic & Respiratory Diseases Department (EPAR), Sorbonne Universités, INSERM, Pierre Louis Institute of Epidemiology & Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Karen Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Vincent WV Jaddoe
- The Generation R Study Group, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Donna Arnett
- College of Public Health, University of Kentucky, Lexington, KY 40536, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sharon LR Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Susan Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | | | - Isabelle Romieu
- Nutrition & Metabolism Section, International Agency for Research on Cancer, Lyon, France
- Center for Research on Population Health, National Institute of Public Health, Mexico
- Hubert Department of Global Health, Emory University, Atlanta, GA 30329, USA
| | - Nona Sotoodehnia
- Department of Medicine, Epidemiology, & Health Services, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98101, USA
| | - Myriam Fornage
- Institute of Molecular Medicine & Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
| | - Alison Motsinger-Reif
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology & Pediatric Allergology, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Center for Genomic Regulation (CRG), Barcelona Institute of Science & Technology, Barcelona, Spain
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA 01702, USA
- Population Sciences Branch, National Heart, Lung, & Blood Institute, National Institutes of Health, Bethesda, MD 01702, USA
| | - Stephanie J London
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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24
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Ma J, Motsinger-Reif A. Current Methods for Quantifying Drug Synergism. Proteom Bioinform 2019; 1:43-48. [PMID: 32043089 PMCID: PMC7010330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The effectiveness of drug combinations for treatment of a variety of complex diseases is well established. "Drug cocktail" treatments are often prescribed to improve the overall efficacy, decrease toxicity, alter pharmacodynamics, etc in an overall treatment strategy. Specifically, if when combined, drugs interact in some way that causes the total effect to be greater than that predicted by their individual potencies, then drugs are considered synergistic. While there are established ways to quantify the impact of drug combinations clinically, it is an open challenge to quantitatively summarize a synergistic interaction. In this paper, we discuss an overview of the current statistical and mathematical methods for the study of drug combination effects, especially drug synergy quantification (where the interaction effect is not just detected, but quantified according to its magnitude). We first introduce two popular reference models for testing to null hypothesis of non-interaction for a combination, including the Bliss independence model and the Loewe additivity model. Then we discuss several methods for quantifying drug synergism. The advantages and disadvantages with these methods are also provided, and finally, we discuss important next directions in this area.
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Affiliation(s)
- Jun Ma
- Bioinformatics Research Center, North Carolina State University
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences
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25
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Ash JR, Kuenemann MA, Rotroff D, Motsinger-Reif A, Fourches D. Cheminformatics approach to exploring and modeling trait-associated metabolite profiles. J Cheminform 2019; 11:43. [PMID: 31236709 PMCID: PMC6591908 DOI: 10.1186/s13321-019-0366-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 06/17/2019] [Indexed: 12/17/2022] Open
Abstract
Developing predictive and transparent approaches to the analysis of metabolite profiles across patient cohorts is of critical importance for understanding the events that trigger or modulate traits of interest (e.g., disease progression, drug metabolism, chemical risk assessment). However, metabolites’ chemical structures are still rarely used in the statistical modeling workflows that establish these trait-metabolite relationships. Herein, we present a novel cheminformatics-based approach capable of identifying predictive, interpretable, and reproducible trait-metabolite relationships. As a proof-of-concept, we utilize a previously published case study consisting of metabolite profiles from non-small-cell lung cancer (NSCLC) adenocarcinoma patients and healthy controls. By characterizing each structurally annotated metabolite using both computed molecular descriptors and patient metabolite concentration profiles, we show that these complementary features enhance the identification and understanding of key metabolites associated with cancer. Ultimately, we built multi-metabolite classification models for assessing patients’ cancer status using specific groups of metabolites identified based on high structural similarity through chemical clustering. We subsequently performed a metabolic pathway enrichment analysis to identify potential mechanistic relationships between metabolites and NSCLC adenocarcinoma. This cheminformatics-inspired approach relies on the metabolites’ structural features and chemical properties to provide critical information about metabolite-trait associations. This method could ultimately facilitate biological understanding and advance research based on metabolomics data, especially with respect to the identification of novel biomarkers. ![]()
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Affiliation(s)
- Jeremy R Ash
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA.,Department of Statistics, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Melaine A Kuenemann
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Daniel Rotroff
- Department of Statistics, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Department of Statistics, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Denis Fourches
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA. .,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
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26
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Kennedy K, Thomas R, Durrant J, Jiang T, Motsinger-Reif A, Breen M. Genome-wide DNA copy number analysis and targeted transcriptional analysis of canine histiocytic malignancies identifies diagnostic signatures and highlights disruption of spindle assembly complex. Chromosome Res 2019; 27:179-202. [PMID: 31011867 DOI: 10.1007/s10577-019-09606-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/16/2022]
Abstract
Canine histiocytic malignancies (HM) are rare across the general dog population, but overrepresented in certain breeds, such as Bernese mountain dog and flat-coated retriever. Accurate diagnosis relies on immunohistochemical staining to rule out histologically similar cancers with different prognoses and treatment strategies (e.g., lymphoma and hemangiosarcoma). HM are generally treatment refractory with overall survival of less than 6 months. A lack of understanding regarding the mechanisms of disease development and progression hinders development of novel therapeutics. While the study of human tumors can benefit veterinary medicine, the rarity of the suggested orthologous disease (dendritic cell sarcoma) precludes this. This study aims to improve the understanding of underlying disease mechanisms using genome-wide DNA copy number and gene expression analysis of spontaneous HM across several dog breeds. Extensive DNA copy number disruption was evident, with losses of segments of chromosomes 16 and 31 detected in 93% and 72% of tumors, respectively. Droplet digital PCR (ddPCR) evaluation of these regions in numerous cancer specimens effectively discriminated HM from other common round cell tumors, including lymphoma and hemangiosarcoma, resulting in a novel, rapid diagnostic aid for veterinary medicine. Transcriptional analysis demonstrated disruption of the spindle assembly complex, which is linked to genomic instability and reduced therapeutic impact in humans. A key signature detected was up-regulation of Matrix Metalloproteinase 9 (MMP9), supported by an immunohistochemistry-based assessment of MMP9 protein levels. Since MMP9 has been linked with rapid metastasis and tumor aggression in humans, the data in this study offer a possible mechanism of aggression in HM.
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Affiliation(s)
- Katherine Kennedy
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.,Sentinel Biomedical Incorporated, Centennial Biomedical Campus, Raleigh, NC, 27607, USA
| | - Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27607, USA
| | - Jessica Durrant
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27607, USA
| | - Tao Jiang
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA.,Department of Statistics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA.,Department of Statistics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA. .,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27607, USA. .,Cancer Genetics Program, University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, 27599, USA. .,Duke Cancer Institute, Duke University, Durham, NC, 27710, USA.
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27
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Crestani E, Leirer J, Motsinger-Reif A, Phipatanakul W, Kaddurah-Daouk R, Chatila TA. Untargeted Metabolomic Profiling Identifies Disease-Specific Pathways in Food Allergy and Asthma. J Allergy Clin Immunol 2019. [DOI: 10.1016/j.jaci.2018.12.778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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MahmoudianDehkordi S, Arnold M, Nho K, Ahmad S, Jia W, Xie G, Louie G, Kueider-Paisley A, Moseley MA, Thompson JW, St John Williams L, Tenenbaum JD, Blach C, Baillie R, Han X, Bhattacharyya S, Toledo JB, Schafferer S, Klein S, Koal T, Risacher SL, Kling MA, Motsinger-Reif A, Rotroff DM, Jack J, Hankemeier T, Bennett DA, De Jager PL, Trojanowski JQ, Shaw LM, Weiner MW, Doraiswamy PM, van Duijn CM, Saykin AJ, Kastenmüller G, Kaddurah-Daouk R. Altered bile acid profile associates with cognitive impairment in Alzheimer's disease-An emerging role for gut microbiome. Alzheimers Dement 2019; 15:76-92. [PMID: 30337151 PMCID: PMC6487485 DOI: 10.1016/j.jalz.2018.07.217] [Citation(s) in RCA: 349] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/01/2018] [Accepted: 07/31/2018] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Increasing evidence suggests a role for the gut microbiome in central nervous system disorders and a specific role for the gut-brain axis in neurodegeneration. Bile acids (BAs), products of cholesterol metabolism and clearance, are produced in the liver and are further metabolized by gut bacteria. They have major regulatory and signaling functions and seem dysregulated in Alzheimer's disease (AD). METHODS Serum levels of 15 primary and secondary BAs and their conjugated forms were measured in 1464 subjects including 370 cognitively normal older adults, 284 with early mild cognitive impairment, 505 with late mild cognitive impairment, and 305 AD cases enrolled in the AD Neuroimaging Initiative. We assessed associations of BA profiles including selected ratios with diagnosis, cognition, and AD-related genetic variants, adjusting for confounders and multiple testing. RESULTS In AD compared to cognitively normal older adults, we observed significantly lower serum concentrations of a primary BA (cholic acid [CA]) and increased levels of the bacterially produced, secondary BA, deoxycholic acid, and its glycine and taurine conjugated forms. An increased ratio of deoxycholic acid:CA, which reflects 7α-dehydroxylation of CA by gut bacteria, strongly associated with cognitive decline, a finding replicated in serum and brain samples in the Rush Religious Orders and Memory and Aging Project. Several genetic variants in immune response-related genes implicated in AD showed associations with BA profiles. DISCUSSION We report for the first time an association between altered BA profile, genetic variants implicated in AD, and cognitive changes in disease using a large multicenter study. These findings warrant further investigation of gut dysbiosis and possible role of gut-liver-brain axis in the pathogenesis of AD.
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Affiliation(s)
| | - Matthias Arnold
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA; Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Wei Jia
- University of Hawaii Cancer Center, Honolulu, HI, USA; Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Guoxiang Xie
- University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Gregory Louie
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | | | - M Arthur Moseley
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Durham, NC, USA
| | - J Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Durham, NC, USA
| | - Lisa St John Williams
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Durham, NC, USA
| | - Jessica D Tenenbaum
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | | | - Xianlin Han
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Sudeepa Bhattacharyya
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jon B Toledo
- Department of Neurology, Houston Methodist Hospital, Houston, TX, USA
| | | | | | | | - Shannon L Risacher
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mitchel Allan Kling
- Behavioral Health Service, Crescenz VA Medical Center and Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Daniel M Rotroff
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - John Jack
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, RA Leiden, The Netherlands
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Columbia University College of Physicians and Surgeons Department of Neurology, Center for Translational & Computational Neuroimmunology, New York, NY, USA
| | - John Q Trojanowski
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leslie M Shaw
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael W Weiner
- Center for Imaging of Neurodegenerative Diseases, Department of Radiology, San Francisco VA Medical Center/University of California San Francisco, San Francisco, CA, USA
| | - P Murali Doraiswamy
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA; Duke Institute of Brain Sciences, Duke University, Durham, NC, USA; Department of Medicine, Duke University, Durham, NC, USA
| | | | - Andrew J Saykin
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany.
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA; Duke Institute of Brain Sciences, Duke University, Durham, NC, USA; Department of Medicine, Duke University, Durham, NC, USA.
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29
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Fox PR, Keene BW, Lamb K, Schober KA, Chetboul V, Luis Fuentes V, Wess G, Payne JR, Hogan DF, Motsinger-Reif A, Häggström J, Trehiou-Sechi E, Fine-Ferreira DM, Nakamura RK, Lee PM, Singh MK, Ware WA, Abbott JA, Culshaw G, Riesen S, Borgarelli M, Lesser MB, Van Israël N, Côté E, Rush JE, Bulmer B, Santilli RA, Vollmar AC, Bossbaly MJ, Quick N, Bussadori C, Bright JM, Estrada AH, Ohad DG, Fernández-Del Palacio MJ, Lunney Brayley J, Schwartz DS, Bové CM, Gordon SG, Jung SW, Brambilla P, Moïse NS, Stauthammer CD, Stepien RL, Quintavalla C, Amberger C, Manczur F, Hung YW, Lobetti R, De Swarte M, Tamborini A, Mooney CT, Oyama MA, Komolov A, Fujii Y, Pariaut R, Uechi M, Tachika Ohara VY. International collaborative study to assess cardiovascular risk and evaluate long-term health in cats with preclinical hypertrophic cardiomyopathy and apparently healthy cats: The REVEAL Study. J Vet Intern Med 2018; 32:930-943. [PMID: 29660848 PMCID: PMC5980443 DOI: 10.1111/jvim.15122] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/04/2018] [Accepted: 02/24/2018] [Indexed: 12/31/2022] Open
Abstract
Background Hypertrophic cardiomyopathy is the most prevalent heart disorder in cats and principal cause of cardiovascular morbidity and mortality. Yet, the impact of preclinical disease is unresolved. Hypothesis/Objectives Observational study to characterize cardiovascular morbidity and survival in cats with preclinical nonobstructive (HCM) and obstructive (HOCM) hypertrophic cardiomyopathy and in apparently healthy cats (AH). Animals One thousand seven hundred and thirty client‐owned cats (430 preclinical HCM; 578 preclinical HOCM; 722 AH). Methods Retrospective multicenter, longitudinal, cohort study. Cats from 21 countries were followed through medical record review and owner or referring veterinarian interviews. Data were analyzed to compare long‐term outcomes, incidence, and risk for congestive heart failure (CHF), arterial thromboembolism (ATE), and cardiovascular death. Results During the study period, CHF, ATE, or both occurred in 30.5% and cardiovascular death in 27.9% of 1008 HCM/HOCM cats. Risk assessed at 1, 5, and 10 years after study entry was 7.0%/3.5%, 19.9%/9.7%, and 23.9%/11.3% for CHF/ATE, and 6.7%, 22.8%, and 28.3% for cardiovascular death, respectively. There were no statistically significant differences between HOCM compared with HCM for cardiovascular morbidity or mortality, time from diagnosis to development of morbidity, or cardiovascular survival. Cats that developed cardiovascular morbidity had short survival (mean ± standard deviation, 1.3 ± 1.7 years). Overall, prolonged longevity was recorded in a minority of preclinical HCM/HOCM cats with 10% reaching 9‐15 years. Conclusions and Clinical Importance Preclinical HCM/HOCM is a global health problem of cats that carries substantial risk for CHF, ATE, and cardiovascular death. This finding underscores the need to identify therapies and monitoring strategies that decrease morbidity and mortality.
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Affiliation(s)
- Philip R Fox
- Department of Cardiology and Caspary Research Institute, The Animal Medical Center, New York, New York, U.S.A
| | - Bruce W Keene
- Department of Clinical Sciences, North Carolina State University, Raleigh, North Carolina, U.S.A
| | | | - Karsten A Schober
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, U.S.A
| | - Valerie Chetboul
- Alfort Cardiology Unit, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort Cedex, France
| | - Virginia Luis Fuentes
- Department of Veterinary Clinical Sciences and Services, The Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom
| | - Gerhard Wess
- Clinic of Small Animal Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Jessie Rose Payne
- Department of Veterinary Clinical Sciences and Services, The Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom
| | - Daniel F Hogan
- Department of Veterinary Clinical Sciences, Purdue University, West Lafayette, Indiana, U.S.A
| | - Alison Motsinger-Reif
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, U.S.A
| | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emilie Trehiou-Sechi
- Alfort Cardiology Unit, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort Cedex, France
| | - Deborah M Fine-Ferreira
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, Missouri, U.S.A
| | - Reid K Nakamura
- Advanced Veterinary Care Center, Lawndale, California, U.S.A
| | - Pamela M Lee
- Department of Cardiology and Caspary Research Institute, The Animal Medical Center, New York, New York, U.S.A
| | - Manreet K Singh
- William R. Pritchard Veterinary Medical Teaching Hospital, University of California-Davis, Davis, California, U.S.A
| | - Wendy A Ware
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, Iowa, U.S.A
| | - Jonathan A Abbott
- Department of Small Animal Clinical Sciences, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, Virginia, U.S.A
| | - Geoffrey Culshaw
- Royal (Dick) SVS Hospital for Small Animals, The University of Edinburgh, Roslin, Midlothian, United Kingdom
| | - Sabine Riesen
- Department for Companion Animals and Horses, University of Veterinary Medicine, Vienna, Austria
| | - Michele Borgarelli
- Department of Clinical Sciences, Kansas State University, Manhattan, Kansas, U.S.A
| | | | | | - Etienne Côté
- Department of Companion Animals, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - John E Rush
- Department of Clinical Sciences, Tufts University, Cummings School of Veterinary Medicine, North Grafton, Massachusetts, U.S.A
| | - Barret Bulmer
- Tufts Veterinary Emergency Treatment & Specialties, Walpole, Massachusetts, U.S.A
| | | | | | | | - Nadine Quick
- Clinic of Small Animal Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Claudio Bussadori
- Department of Cardiology, Clinica Veterinaria Gran Sasso, Milan, Italy
| | - Janice M Bright
- Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, U.S.A
| | - Amara H Estrada
- Department of Small Animal Clinical Sciences, University of Florida, Gainesville, Florida
| | - Dan G Ohad
- Department of Clinical Sciences, The Koret School of Veterinary Medicine, Rehovot, Israel
| | | | | | - Denise S Schwartz
- Department of Internal Medicine, University of São Paulo, São Paulo, Brazil
| | - Christina M Bové
- Department of Clinical Studies, University of Guelph, Guelph, Ontario, Canada
| | - Sonya G Gordon
- Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, U.S.A
| | - Seung Woo Jung
- William R. Pritchard Veterinary Medical Teaching Hospital, University of California-Davis, Davis, California, U.S.A
| | - Paola Brambilla
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - N Sydney Moïse
- Department of Clinical Sciences, Cornell University, Ithaca, New York, U.S.A
| | | | - Rebecca L Stepien
- Department of Medical Sciences, University of Wisconsin School of Veterinary Medicine, Madison, Wisconsin, U.S.A
| | | | | | - Ferenc Manczur
- Department of Internal Medicine, University of Veterinary Medicine, Budapest, Hungary
| | | | - Remo Lobetti
- Bryanston Veterinary Hospital, Bryanston, South Africa
| | - Marie De Swarte
- University College Dublin Veterinary Hospital, University College Dublin, Dublin, Ireland
| | - Alice Tamborini
- University College Dublin Veterinary Hospital, University College Dublin, Dublin, Ireland
| | - Carmel T Mooney
- University College Dublin Veterinary Hospital, University College Dublin, Dublin, Ireland
| | - Mark A Oyama
- Department of Clinical Studies, University of Pennsylvania, Philadelphia, Pennsylvania, U.S.A
| | | | - Yoko Fujii
- Azabu University, Sagamihara, Kanagawa, Japan
| | - Romain Pariaut
- Department of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, Louisiana, U.S.A
| | - Masami Uechi
- Jasmine Animal Cardiovascular Center, Yokohama, Kanagawa, Japan
| | - Victoria Yukie Tachika Ohara
- Department of Medicine, Surgery and Zootechnics for Small Species, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Shahin MH, Gong Y, Frye RF, Rotroff DM, Beitelshees AL, Baillie RA, Chapman AB, Gums JG, Turner ST, Boerwinkle E, Motsinger-Reif A, Fiehn O, Cooper-DeHoff RM, Han X, Kaddurah-Daouk R, Johnson JA. Sphingolipid Metabolic Pathway Impacts Thiazide Diuretics Blood Pressure Response: Insights From Genomics, Metabolomics, and Lipidomics. J Am Heart Assoc 2017; 7:JAHA.117.006656. [PMID: 29288159 PMCID: PMC5778957 DOI: 10.1161/jaha.117.006656] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Background Although hydrochlorothiazide (HCTZ) is a well‐established first‐line antihypertensive in the United States, <50% of HCTZ treated patients achieve blood pressure (BP) control. Thus, identifying biomarkers that could predict the BP response to HCTZ is critically important. In this study, we utilized metabolomics, genomics, and lipidomics to identify novel pathways and biomarkers associated with HCTZ BP response. Methods and Results First, we conducted a pathway analysis for 13 metabolites we recently identified to be significantly associated with HCTZ BP response. From this analysis, we found the sphingolipid metabolic pathway as the most significant pathway (P=5.8E‐05). Testing 78 variants, within 14 genes involved in the sphingolipid metabolic canonical pathway, with the BP response to HCTZ identified variant rs6078905, within the SPTLC3 gene, as a novel biomarker significantly associated with the BP response to HCTZ in whites (n=228). We found that rs6078905 C‐allele carriers had a better BP response to HCTZ versus noncarriers (∆SBP/∆DBP: −11.4/−6.9 versus −6.8/−3.5 mm Hg; ∆SBP P=6.7E‐04; ∆DBP P=4.8E‐04). Additionally, in blacks (n=148), we found genetic signals in the SPTLC3 genomic region significantly associated with the BP response to HCTZ (P<0.05). Last, we observed that rs6078905 significantly affects the baseline level of 4 sphingomyelins (N24:2, N24:3, N16:1, and N22:1; false discovery rate <0.05), from which N24:2 sphingomyelin has a significant correlation with both HCTZ DBP‐response (r=−0.42; P=7E‐03) and SBP‐response (r=−0.36; P=2E‐02). Conclusions This study provides insight into potential pharmacometabolomic and genetic mechanisms underlying HCTZ BP response and suggests that SPTLC3 is a potential determinant of the BP response to HCTZ. Clinical Trial Registration URL: http://www.clinicaltrials.gov. Unique identifier: NCT00246519.
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Affiliation(s)
- Mohamed H Shahin
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL
| | - Reginald F Frye
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL
| | - Daniel M Rotroff
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC
| | | | | | | | - John G Gums
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL
| | | | - Eric Boerwinkle
- Human Genetics Center and Institute for Molecular Medicine, University of Texas Health Science Center, Houston, TX
| | | | - Oliver Fiehn
- Genome Center, University of California at Davis, CA.,Biochemistry Department, King Abdulaziz University, Jeddah, Saudi-Arabia
| | - Rhonda M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL
| | - Xianlin Han
- Sanford-Burnham Medical Research Institute, Orlando, FL
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioural Sciences and Department of Medicine, Duke University, Durham, NC
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL
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31
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Nguyen TV, Reuter JM, Gaikwad NW, Rotroff DM, Kucera HR, Motsinger-Reif A, Smith CP, Nieman LK, Rubinow DR, Kaddurah-Daouk R, Schmidt PJ. The steroid metabolome in women with premenstrual dysphoric disorder during GnRH agonist-induced ovarian suppression: effects of estradiol and progesterone addback. Transl Psychiatry 2017; 7:e1193. [PMID: 28786978 PMCID: PMC5611719 DOI: 10.1038/tp.2017.146] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/05/2017] [Accepted: 05/26/2017] [Indexed: 01/08/2023] Open
Abstract
Clinical evidence suggests that symptoms in premenstrual dysphoric disorder (PMDD) reflect abnormal responsivity to ovarian steroids. This differential steroid sensitivity could be underpinned by abnormal processing of the steroid signal. We used a pharmacometabolomics approach in women with prospectively confirmed PMDD (n=15) and controls without menstrual cycle-related affective symptoms (n=15). All were medication-free with normal menstrual cycle lengths. Notably, women with PMDD were required to show hormone sensitivity in an ovarian suppression protocol. Ovarian suppression was induced for 6 months with gonadotropin-releasing hormone (GnRH)-agonist (Lupron); after 3 months all were randomized to 4 weeks of estradiol (E2) or progesterone (P4). After a 2-week washout, a crossover was performed. Liquid chromatography/tandem mass spectrometry measured 49 steroid metabolites in serum. Values were excluded if >40% were below the limit of detectability (n=21). Analyses were performed with Wilcoxon rank-sum tests using false-discovery rate (q<0.2) for multiple comparisons. PMDD and controls had similar basal levels of metabolites during Lupron and P4-derived neurosteroids during Lupron or E2/P4 conditions. Both groups had significant increases in several steroid metabolites compared with the Lupron alone condition after treatment with E2 (that is, estrone-SO4 (q=0.039 and q=0.002, respectively) and estradiol-3-SO4 (q=0.166 and q=0.001, respectively)) and after treatment with P4 (that is, allopregnanolone (q=0.001 for both PMDD and controls), pregnanediol (q=0.077 and q=0.030, respectively) and cortexone (q=0.118 and q=0.157, respectively). Only sulfated steroid metabolites showed significant diagnosis-related differences. During Lupron plus E2 treatment, women with PMDD had a significantly attenuated increase in E2-3-sulfate (q=0.035) compared with control women, and during Lupron plus P4 treatment a decrease in DHEA-sulfate (q=0.07) compared with an increase in controls. Significant effects of E2 addback compared with Lupron were observed in women with PMDD who had significant decreases in DHEA-sulfate (q=0.065) and pregnenolone sulfate (q=0.076), whereas controls had nonsignificant increases (however, these differences did not meet statistical significance for a between diagnosis effect). Alterations of sulfotransferase activity could contribute to the differential steroid sensitivity in PMDD. Importantly, no differences in the formation of P4-derived neurosteroids were observed in this otherwise highly selected sample of women studied under controlled hormone exposures.
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Affiliation(s)
- T V Nguyen
- Behavioral Endocrinology Branch, NIMH IRP/NIH/HHS, Bethesda, MD, USA
- Department of Psychiatry and Obstetrics-Gynecology, McGill University Health Center, Montreal, QC, Canada
| | - J M Reuter
- Behavioral Endocrinology Branch, NIMH IRP/NIH/HHS, Bethesda, MD, USA
| | - N W Gaikwad
- Department of Nutrition and Environmental Toxicology, West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
| | - D M Rotroff
- Department of Biostatistics, Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - H R Kucera
- Department of Nutrition and Environmental Toxicology, West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
| | - A Motsinger-Reif
- Department of Biostatistics, Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - C P Smith
- Department of Biostatistics, Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - L K Nieman
- Diabetes, Endocrine and Obesity Branch, NIDDK, NIH, DHSS, Bethesda, MD, USA
| | - D R Rubinow
- Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - R Kaddurah-Daouk
- Department of Psychiatry, Duke University Medical Center, Durham, NC, USA
- Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | - P J Schmidt
- Behavioral Endocrinology Branch, NIMH IRP/NIH/HHS, Bethesda, MD, USA
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Toledo JB, Arnold M, Kastenmüller G, Chang R, Baillie RA, Han X, Thambisetty M, Tenenbaum JD, Suhre K, Thompson JW, John-Williams LS, MahmoudianDehkordi S, Rotroff DM, Jack JR, Motsinger-Reif A, Risacher SL, Blach C, Lucas JE, Massaro T, Louie G, Zhu H, Dallmann G, Klavins K, Koal T, Kim S, Nho K, Shen L, Casanova R, Varma S, Legido-Quigley C, Moseley MA, Zhu K, Henrion MYR, van der Lee SJ, Harms AC, Demirkan A, Hankemeier T, van Duijn CM, Trojanowski JQ, Shaw LM, Saykin AJ, Weiner MW, Doraiswamy PM, Kaddurah-Daouk R. Metabolic network failures in Alzheimer's disease: A biochemical road map. Alzheimers Dement 2017; 13:965-984. [PMID: 28341160 DOI: 10.1016/j.jalz.2017.01.020] [Citation(s) in RCA: 292] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The Alzheimer's Disease Research Summits of 2012 and 2015 incorporated experts from academia, industry, and nonprofit organizations to develop new research directions to transform our understanding of Alzheimer's disease (AD) and propel the development of critically needed therapies. In response to their recommendations, big data at multiple levels are being generated and integrated to study network failures in disease. We used metabolomics as a global biochemical approach to identify peripheral metabolic changes in AD patients and correlate them to cerebrospinal fluid pathology markers, imaging features, and cognitive performance. METHODS Fasting serum samples from the Alzheimer's Disease Neuroimaging Initiative (199 control, 356 mild cognitive impairment, and 175 AD participants) were analyzed using the AbsoluteIDQ-p180 kit. Performance was validated in blinded replicates, and values were medication adjusted. RESULTS Multivariable-adjusted analyses showed that sphingomyelins and ether-containing phosphatidylcholines were altered in preclinical biomarker-defined AD stages, whereas acylcarnitines and several amines, including the branched-chain amino acid valine and α-aminoadipic acid, changed in symptomatic stages. Several of the analytes showed consistent associations in the Rotterdam, Erasmus Rucphen Family, and Indiana Memory and Aging Studies. Partial correlation networks constructed for Aβ1-42, tau, imaging, and cognitive changes provided initial biochemical insights for disease-related processes. Coexpression networks interconnected key metabolic effectors of disease. DISCUSSION Metabolomics identified key disease-related metabolic changes and disease-progression-related changes. Defining metabolic changes during AD disease trajectory and its relationship to clinical phenotypes provides a powerful roadmap for drug and biomarker discovery.
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Affiliation(s)
- Jon B Toledo
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Neurology, Houston Methodist Hospital, Houston, TX, USA.
| | - Matthias Arnold
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Rui Chang
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Xianlin Han
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, USA
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Unit, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jessica D Tenenbaum
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Department of Physiology and Biophysics, Weill Cornell Medical College, Qatar, Doha, Qatar
| | - J Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Lisa St John-Williams
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Siamak MahmoudianDehkordi
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Daniel M Rotroff
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - John R Jack
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Shannon L Risacher
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; The Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA; Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Joseph E Lucas
- Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA
| | - Tyler Massaro
- Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA
| | - Gregory Louie
- Department of Psychiatry, Duke University, Durham, NC, USA; Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | - Hongjie Zhu
- Department of Psychiatry, Duke University, Durham, NC, USA; Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | | | | | | | - Sungeun Kim
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; The Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; The Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Li Shen
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; The Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ramon Casanova
- Clinical and Translational Neuroscience Unit, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Sudhir Varma
- Clinical and Translational Neuroscience Unit, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | | | - M Arthur Moseley
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Kuixi Zhu
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marc Y R Henrion
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Amy C Harms
- Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Ayse Demirkan
- Department of Epidemiology, ErasmusMC, Rotterdam, The Netherlands
| | - Thomas Hankemeier
- Department of Epidemiology, ErasmusMC, Rotterdam, The Netherlands; Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, ErasmusMC, Rotterdam, The Netherlands; Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - John Q Trojanowski
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leslie M Shaw
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; The Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael W Weiner
- Department of Radiology, Center for Imaging of Neurodegenerative Diseases, San Francisco VA Medical Center/University of California San Francisco, San Francisco, CA, USA
| | - P Murali Doraiswamy
- Department of Psychiatry, Duke University, Durham, NC, USA; Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry, Duke University, Durham, NC, USA; Duke Institute for Brain Sciences, Duke University, Durham, NC, USA; Department of Medicine, Duke University Medical Center, Durham, NC, USA.
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Friedenberg SG, Chdid L, Keene B, Sherry B, Motsinger-Reif A, Meurs KM. Use of RNA-seq to identify cardiac genes and gene pathways differentially expressed between dogs with and without dilated cardiomyopathy. Am J Vet Res 2017; 77:693-9. [PMID: 27347821 DOI: 10.2460/ajvr.77.7.693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To identify cardiac tissue genes and gene pathways differentially expressed between dogs with and without dilated cardiomyopathy (DCM). ANIMALS 8 dogs with and 5 dogs without DCM. PROCEDURES Following euthanasia, samples of left ventricular myocardium were collected from each dog. Total RNA was extracted from tissue samples, and RNA sequencing was performed on each sample. Samples from dogs with and without DCM were grouped to identify genes that were differentially regulated between the 2 populations. Overrepresentation analysis was performed on upregulated and downregulated gene sets to identify altered molecular pathways in dogs with DCM. RESULTS Genes involved in cellular energy metabolism, especially metabolism of carbohydrates and fats, were significantly downregulated in dogs with DCM. Expression of cardiac structural proteins was also altered in affected dogs. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that RNA sequencing may provide important insights into the pathogenesis of DCM in dogs and highlight pathways that should be explored to identify causative mutations and develop novel therapeutic interventions.
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Rotroff DM, Joubert BR, Marvel SW, Håberg SE, Wu MC, Nilsen RM, Ueland PM, Nystad W, London SJ, Motsinger-Reif A. Maternal smoking impacts key biological pathways in newborns through epigenetic modification in Utero. BMC Genomics 2016; 17:976. [PMID: 27887572 PMCID: PMC5124223 DOI: 10.1186/s12864-016-3310-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 11/17/2016] [Indexed: 01/29/2023] Open
Abstract
Background Children exposed to maternal smoking during pregnancy exhibit increased risk for many adverse health effects. Maternal smoking influences methylation in newborns at specific CpG sites (CpGs). Here, we extend evaluation of individual CpGs to gene-level and pathway-level analyses among 1062 participants in the Norwegian Mother and Child Cohort Study (MoBa) using the Illumina 450 K platform to measure methylation in newborn DNA and maternal smoking in pregnancy, assessed using the biomarker, plasma cotinine. We used novel implementations of bioinformatics tools to collapse epigenome-wide methylation data into gene- and pathway-level effects to test whether exposure to maternal smoking in utero differentially methylated CpGs in genes enriched in biologic pathways. Unlike most pathway analysis applications, our approach allows replication in an independent cohort. Results Data on 485,577 CpGs, mapping to a total of 20,199 genes, were used to create gene scores that were tested for association with maternal plasma cotinine levels using Sequence Kernel Association Test (SKAT), and 15 genes were found to be associated (q < 0.25). Six of these 15 genes (GFI1, MYO1G, CYP1A1, RUNX1, LCTL, and AHRR) contained individual CpGs that were differentially methylated with regards to cotinine levels (p < 1.06 × 10−7). Nine of the 15 genes (FCRLA, MIR641, SLC25A24, TRAK1, C1orf180, ITLN2, GLIS1, LRFN1, and MIR451) were associated with cotinine at the gene-level (q < 0.25) but had no genome-wide significant individual CpGs (p > 1.06 × 10−7). Pathway analyses using gene scores resulted in 51 significantly associated pathways, which we tested for replication in an independent cohort (q < 0.05). Of those 32 replicated in an independent cohort, which clustered into six groups. The largest cluster consisted of pathways related to cancer, cell cycle, ERα receptor signaling, and angiogenesis. The second cluster, organized into five smaller pathway groups, related to immune system function, such as T-cell regulation and other white blood cell related pathways. Conclusions Here we use novel implementations of bioinformatics tools to determine biological pathways impacted through epigenetic changes in utero by maternal smoking in 1062 participants in the MoBa, and successfully replicate these findings in an independent cohort. The results provide new insight into biological mechanisms that may contribute to adverse health effects from exposure to tobacco smoke in utero. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3310-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel M Rotroff
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Bonnie R Joubert
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, PO Box 12233, MD A3-05, Research Triangle Park, NC, 27709, USA
| | - Skylar W Marvel
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | | | - Michael C Wu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Roy M Nilsen
- Centre for Clinical Research, Haukeland University Hospital, Bergen, Norway
| | - Per M Ueland
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Laboratory of Clinical Biochemistry, Haukeland University Hospital, Bergen, Norway
| | | | - Stephanie J London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, PO Box 12233, MD A3-05, Research Triangle Park, NC, 27709, USA.
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Statistics, North Carolina State University, Raleigh, NC, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA
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Scott Chialvo CH, Che R, Reif D, Motsinger-Reif A, Reed LK. Eigenvector metabolite analysis reveals dietary effects on the association among metabolite correlation patterns, gene expression, and phenotypes. Metabolomics 2016; 12:167. [PMID: 28845148 PMCID: PMC5568542 DOI: 10.1007/s11306-016-1117-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION 'Multi-omics' datasets obtained from an organism of interest reared under different environmental treatments are increasingly common. Identifying the links among metabolites and transcripts can help to elucidate our understanding of the impact of environment at different levels within the organism. However, many methods for characterizing physiological connections cannot address unidentified metabolites. OBJECTIVES Here, we use Eigenvector Metabolite Analysis (EvMA) to examine links between metabolomic, transcriptomic, and phenotypic variation data and to assess the impact of environmental factors on these associations. Unlike other methods, EvMA can be used to analyze datasets that include unidentified metabolites and unannotated transcripts. METHODS To demonstrate the utility of EvMA, we analyzed metabolomic, transcriptomic, and phenotypic datasets produced from 20 Drosophila melanogaster genotypes reared on four dietary treatments. We used a hierarchical distance-based method to cluster the metabolites. The links between metabolite clusters, gene expression, and overt phenotypes were characterized using the eigenmetabolite (first principal component) of each cluster. RESULTS EvMA recovered chemically related groups of metabolites within the clusters. Using the eigenmetabolite, we identified genes and phenotypes that significantly correlated with each cluster. EvMA identifies new connections between the phenotypes, metabolites, and gene transcripts. Conclusion EvMA provides a simple method to identify correlations between metabolites, gene expression, and phenotypes, which can allow us to partition multivariate datasets into meaningful biological modules and identify under-studied metabolites and unannotated gene transcripts that may be central to important biological processes. This can be used to inform our understanding of the effect of environmental mechanisms underlying physiological states of interest.
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Affiliation(s)
- Clare H Scott Chialvo
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35487, USA
| | - Ronglin Che
- Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA
| | - David Reif
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Laura K Reed
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35487, USA
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McLaughlin CM, Marks SL, Dorman DC, Motsinger-Reif A, Hanel RM. Thromboelastographic monitoring of the effect of unfractionated heparin in healthy dogs. J Vet Emerg Crit Care (San Antonio) 2016; 27:71-81. [PMID: 27732770 DOI: 10.1111/vec.12526] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/26/2016] [Accepted: 04/18/2016] [Indexed: 01/13/2023]
Abstract
OBJECTIVE To characterize the correlation between thromboelastography (TEG) variables using strong activators and anti-Xa (AXa) activity in healthy dogs administered subcutaneous unfractionated heparin (UFH). DESIGN Prospective experimental study. SETTING University research facility. ANIMALS Eight adult random-source male dogs. INTERVENTION Dogs were randomized to receive subcutaneous UFH at 200, 250, or 300 IU/kg every 8 hours for a total of 10 injections. Blood samples were collected at time 0 (preheparin) and 3, 6, and 8 hours after the 1st (Day 1) and 10th (Day 4) UFH injection. After the 8-hour blood sample was obtained on day 4, a 100 IU/kg IV bolus of UFH was administered and an additional blood sample was collected 1 hour later (hour 9). AXa activity, activated partial thromboplastin time (aPTT), and TEG (with up to 5 activators) were performed at each time point. Modes of activation for TEG included recalcified (Ca), Ca with heparinase (CaH), CaH and tissue factor 1:3600 (CTF3600H), Ca with tissue factor 1:100 (CTF100), and RapidTEG. Spearman rank correlations were calculated for each of the aforementioned parameters and the AXa activity. P-values were corrected for multiple comparisons with a Bonferroni correction. MEASUREMENTS AND MAIN RESULTS Significant correlations were found between AXa activity and the TEG R values generated with CTF100 (R = 0.83, P ≤ 0.0001) and RapidTEG (R = 0.90, P < 0.0001), as well as both forms of aPTT measurement (R = 0.86 and 0.84, P < 0.0001). CONCLUSIONS This study demonstrates that TEG variables derived using robust activation correlate with AXa activity as well as aPTT and have the potential to be used for monitoring UFH therapy in healthy dogs. Future studies are warranted to evaluate its diagnostic utility in critically ill animals.
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Affiliation(s)
- Christopher M McLaughlin
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine and the NCSU Bioinformatics Research Center, Raleigh, NC, 27606
| | - Steven L Marks
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine and the NCSU Bioinformatics Research Center, Raleigh, NC, 27606
| | - David C Dorman
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine and the NCSU Bioinformatics Research Center, Raleigh, NC, 27606
| | - Alison Motsinger-Reif
- Department of Statistics, NCSU College of Physical and Mathematical Sciences, North Carolina State University, Raleigh, NC, 27606
| | - Rita M Hanel
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine and the NCSU Bioinformatics Research Center, Raleigh, NC, 27606
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Rotroff DM, Corum DG, Motsinger-Reif A, Fiehn O, Bottrel N, Drevets WC, Singh J, Salvadore G, Kaddurah-Daouk R. Metabolomic signatures of drug response phenotypes for ketamine and esketamine in subjects with refractory major depressive disorder: new mechanistic insights for rapid acting antidepressants. Transl Psychiatry 2016; 6:e894. [PMID: 27648916 PMCID: PMC5048196 DOI: 10.1038/tp.2016.145] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 06/01/2016] [Indexed: 12/22/2022] Open
Abstract
Ketamine, at sub-anesthetic doses, is reported to rapidly decrease depression symptoms in patients with treatment-resistant major depressive disorder (MDD). Many patients do not respond to currently available antidepressants, (for example, serotonin reuptake inhibitors), making ketamine and its enantiomer, esketamine, potentially attractive options for treatment-resistant MDD. Although mechanisms by which ketamine/esketamine may produce antidepressant effects have been hypothesized on the basis of preclinical data, the neurobiological correlates of the rapid therapeutic response observed in patients receiving treatment have not been established. Here we use a pharmacometabolomics approach to map global metabolic effects of these compounds in treatment-refractory MDD patients upon 2 h from infusion with ketamine (n=33) or its S-enantiomer, esketamine (n=20). The effects of esketamine on metabolism were retested in the same subjects following a second exposure administered 4 days later. Two complementary metabolomics platforms were used to provide broad biochemical coverage. In addition, we investigated whether changes in particular metabolites correlated with treatment outcome. Both drugs altered metabolites related to tryptophan metabolism (for example, indole-3-acetate and methionine) and/or the urea cycle (for example, citrulline, arginine and ornithine) at 2 h post infusion (q<0.25). In addition, we observed changes in glutamate and circulating phospholipids that were significantly associated with decreases in depression severity. These data provide new insights into the mechanism underlying the rapid antidepressant effects of ketamine and esketamine, and constitute some of the first detailed metabolomics mapping for these promising therapies.
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Affiliation(s)
- D M Rotroff
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - D G Corum
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - A Motsinger-Reif
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - O Fiehn
- UC Davis Genome Center, University of California Davis, Davis, CA, USA
- Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - N Bottrel
- Department of Neuroscience, Janssen Research and Development, Titusville, NJ, USA
| | - W C Drevets
- Department of Neuroscience, Janssen Research and Development, Titusville, NJ, USA
| | - J Singh
- Department of Neuroscience, Janssen Research and Development, San Diego CA, USA
| | - G Salvadore
- Department of Neuroscience, Janssen Research and Development, Titusville, NJ, USA
| | - R Kaddurah-Daouk
- Department of Psychiatry, Duke University Medical Center, Durham NC, USA
- Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
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Roode SC, Rotroff D, Richards KL, Moore P, Motsinger-Reif A, Okamura Y, Mizuno T, Tsujimoto H, Suter SE, Breen M. Comprehensive genomic characterization of five canine lymphoid tumor cell lines. BMC Vet Res 2016; 12:207. [PMID: 27639374 PMCID: PMC5027081 DOI: 10.1186/s12917-016-0836-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/08/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Leukemia/lymphoma cell lines have been critical in the investigation of the pathogenesis and therapy of hematological malignancies. While human LL cell lines have generally been found to recapitulate the primary tumors from which they were derived, appropriate characterization including cytogenetic and transcriptional assessment is crucial for assessing their clinical predictive value. RESULTS In the following study, five canine LL cell lines, CLBL-1, Ema, TL-1 (Nody-1), UL-1, and 3132, were characterized using extensive immunophenotyping, karyotypic analysis, oligonucleotide array comparative genomic hybridization (oaCGH), and gene expression profiling. Genome-wide DNA copy number data from the cell lines were also directly compared with 299 primary canine round cell tumors to determine whether the cell lines represent primary tumors, and, if so, what subtype each most closely resembled. CONCLUSIONS Based on integrated analyses, CLBL-1 was classified as B-cell lymphoma, Ema and TL-1 as T-cell lymphoma, and UL-1 as T-cell acute lymphoblastic leukemia. 3132, originally classified as a B-cell lymphoma, was reclassified as a histiocytic sarcoma based on characteristic cytogenomic properties. In combination, these data begin to elucidate the clinical predictive value of these cell lines which will enhance the appropriate selection of in vitro models for future studies of canine hematological malignancies.
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Affiliation(s)
- Sarah C Roode
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, CVM Research Building - Room 348, 1060 William Moore Drive, Raleigh, 27607, NC, USA
| | - Daniel Rotroff
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Kristy L Richards
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
- Cancer Genetics Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- KLR current address: Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Peter Moore
- Department of Pathology, Microbiology, and Immunology, College of Veterinary Medicine, University of California, Davis, CA, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
| | - Yasuhiko Okamura
- Veterinary Teaching Hospital, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Takuya Mizuno
- Laboratory of Veterinary Internal Medicine, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
| | - Hajime Tsujimoto
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Japan
| | - Steven E Suter
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.
- Cancer Genetics Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, CVM Research Building - Room 308, 1051 William Moore Drive, Raleigh, NC, 27607, USA.
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, CVM Research Building - Room 348, 1060 William Moore Drive, Raleigh, 27607, NC, USA.
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.
- Cancer Genetics Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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Shahin MH, Gong Y, McDonough CW, Rotroff DM, Beitelshees AL, Garrett TJ, Gums JG, Motsinger-Reif A, Chapman AB, Turner ST, Boerwinkle E, Frye RF, Fiehn O, Cooper-DeHoff RM, Kaddurah-Daouk R, Johnson JA. A Genetic Response Score for Hydrochlorothiazide Use: Insights From Genomics and Metabolomics Integration. Hypertension 2016; 68:621-9. [PMID: 27381900 DOI: 10.1161/hypertensionaha.116.07328] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/05/2016] [Indexed: 12/21/2022]
Abstract
Hydrochlorothiazide is among the most commonly prescribed antihypertensives; yet, <50% of hydrochlorothiazide-treated patients achieve blood pressure (BP) control. Herein, we integrated metabolomic and genomic profiles of hydrochlorothiazide-treated patients to identify novel genetic markers associated with hydrochlorothiazide BP response. The primary analysis included 228 white hypertensives treated with hydrochlorothiazide from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) study. Genome-wide analysis was conducted using Illumina Omni 1 mol/L-Quad Chip, and untargeted metabolomics was performed on baseline fasting plasma samples using a gas chromatography-time-of-flight mass spectrometry platform. We found 13 metabolites significantly associated with hydrochlorothiazide systolic BP (SBP) and diastolic BP (DBP) responses (false discovery rate, <0.05). In addition, integrating genomic and metabolomic data revealed 3 polymorphisms (rs2727563 PRKAG2, rs12604940 DCC, and rs13262930 EPHX2) along with arachidonic acid, converging in the netrin signaling pathway (P=1×10(-5)), as potential markers, significantly influencing hydrochlorothiazide BP response. We successfully replicated the 3 genetic signals in 212 white hypertensives treated with hydrochlorothiazide and created a response score by summing their BP-lowering alleles. We found patients carrying 1 response allele had a significantly lower response than carriers of 6 alleles (∆SBP/∆DBP: -1.5/1.2 versus -16.3/-10.4 mm Hg, respectively, SBP score, P=1×10(-8) and DBP score, P=3×10(-9)). This score explained 11.3% and 11.9% of the variability in hydrochlorothiazide SBP and DBP responses, respectively, and was further validated in another independent study of 196 whites treated with hydrochlorothiazide (DBP score, P=0.03; SBP score, P=0.07). This study suggests that PRKAG2, DCC, and EPHX2 might be important determinants of hydrochlorothiazide BP response.
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Affiliation(s)
- Mohamed H Shahin
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Yan Gong
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Caitrin W McDonough
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Daniel M Rotroff
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Amber L Beitelshees
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Timothy J Garrett
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - John G Gums
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Alison Motsinger-Reif
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Arlene B Chapman
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Stephen T Turner
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Eric Boerwinkle
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Reginald F Frye
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Oliver Fiehn
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Rhonda M Cooper-DeHoff
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Rima Kaddurah-Daouk
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.)
| | - Julie A Johnson
- From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (M.H.S., Y.G., C.W.M., J.G.G., R.F.F., R.M.C.-D., J.A.J.) and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine (T.J.G.), University of Florida, Gainesville; Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh (D.M.R., A.M.-R.); Department of Medicine, University of Maryland, Baltimore (A.L.B.); Department of Medicine, Emory University, Atlanta, GA (A.B.C.); Division of Nephrology and Hypertension, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN (S.T.T.); Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, (E.B.); Department of Molecular and Cellular Biology and Genome Center, University of California, Davis (O.F.); and Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC (R.K.-D.).
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Kim S, Toledo JB, Nho K, Risacher SL, Shen L, Thompson JW, St. John Williams L, Tenenbaum J, Han X, Baillie RA, Thambisetty M, Casanova R, Varma S, Legido-Quigley C, Mahmoudiandehkordi S, Motsinger-Reif A, Zhu H, Kastenmüller G, Suhre K, Dallmann G, Klavins K, Koal T, Moseley MA, Trojanowski JQ, Shaw LM, Weiner MW, Doraiswamy M, Kaddurah-Daouk RF, Saykin AJ. F1‐02‐02: Genetic Influence on Levels of Targeted Metabolites Associated with Alzheimer’s Disease. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Sungeun Kim
- Indiana University School of MedicineIndianapolisIN USA
| | | | - Kwangsik Nho
- Indiana University School of MedicineIndianapolisIN USA
| | | | - Li Shen
- Indiana University School of MedicineIndianapolisIN USA
| | | | | | | | - Xianlin Han
- Sanford-Burnham Medical Research InstituteOrlandoFL USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Leslie M. Shaw
- Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaPA USA
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Reinhart JM, Motsinger-Reif A, Dickey A, Yale S, Trepanier LA. Genome-Wide Association Study in Immunocompetent Patients with Delayed Hypersensitivity to Sulfonamide Antimicrobials. PLoS One 2016; 11:e0156000. [PMID: 27272151 PMCID: PMC4896425 DOI: 10.1371/journal.pone.0156000] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 05/06/2016] [Indexed: 01/11/2023] Open
Abstract
Background Hypersensitivity (HS) reactions to sulfonamide antibiotics occur uncommonly, but with potentially severe clinical manifestations. A familial predisposition to sulfonamide HS is suspected, but robust predictive genetic risk factors have yet to be identified. Strongly linked genetic polymorphisms have been used clinically as screening tests for other HS reactions prior to administration of high-risk drugs. Objective The purpose of this study was to evaluate for genetic risk of sulfonamide HS in the immunocompetent population using genome-wide association. Methods Ninety-one patients with symptoms after trimethoprim-sulfamethoxazole (TMP-SMX) attributable to “probable” drug HS based on medical record review and the Naranjo Adverse Drug Reaction Probability Scale, and 184 age- and sex-matched patients who tolerated a therapeutic course of TMP-SMX, were included in a genome-wide association study using both common and rare variant techniques. Additionally, two subgroups of HS patients with a more refined clinical phenotype (fever and rash; or fever, rash and eosinophilia) were evaluated separately. Results For the full dataset, no single nucleotide polymorphisms were suggestive of or reached genome-wide significance in the common variant analysis, nor was any genetic locus significant in the rare variant analysis. A single, possible gene locus association (COL12A1) was identified in the rare variant analysis for patients with both fever and rash, but the sample size was very small in this subgroup (n = 16), and this may be a false positive finding. No other significant associations were found for the subgroups. Conclusions No convincing genetic risk factors for sulfonamide HS were identified in this population. These negative findings may be due to challenges in accurately confirming the phenotype in exanthematous drug eruptions, or to unidentified gene-environment interactions influencing sulfonamide HS.
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Affiliation(s)
- Jennifer M. Reinhart
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Allison Dickey
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Steven Yale
- Marshfield Clinic Research Foundation, Marshfield, Wisconsin, United States of America
| | - Lauren A. Trepanier
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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He YJ, Winham SJ, Hoskins JM, Glass S, Paul J, Brown R, Motsinger-Reif A, McLeod HL. Carboplatin/taxane-induced gastrointestinal toxicity: a pharmacogenomics study on the SCOTROC1 trial. Pharmacogenomics J 2016; 16:243-8. [PMID: 26194361 DOI: 10.1038/tpj.2015.52] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 05/05/2015] [Accepted: 06/03/2015] [Indexed: 01/13/2023]
Abstract
Carboplatin/taxane combination is first-line therapy for ovarian cancer. However, patients can encounter treatment delays, impaired quality of life, even death because of chemotherapy-induced gastrointestinal (GI) toxicity. A candidate gene study was conducted to assess potential association of genetic variants with GI toxicity in 808 patients who received carboplatin/taxane in the Scottish Randomized Trial in Ovarian Cancer 1 (SCOTROC1). Patients were randomized into discovery and validation cohorts consisting of 404 patients each. Clinical covariates and genetic variants associated with grade III/IV GI toxicity in discovery cohort were evaluated in replication cohort. Chemotherapy-induced GI toxicity was significantly associated with seven single-nucleotide polymorphisms in the ATP7B, GSR, VEGFA and SCN10A genes. Patients with risk genotypes were at 1.53 to 18.01 higher odds to develop carboplatin/taxane-induced GI toxicity (P<0.01). Variants in the VEGF gene were marginally associated with survival time. Our data provide potential targets for modulation/inhibition of GI toxicity in ovarian cancer patients.
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Affiliation(s)
- Y J He
- Department of Clinical Pharmacology, Xiang-Ya Hospital, Central South University, Changsha, China
- Pharmacogenetics Research institute, Central South University, Changsha, China
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC, USA
- Moffitt Cancer Center, DeBartolo Family Personalized Medicine Institute, Tampa, FL, USA
| | - S J Winham
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - J M Hoskins
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC, USA
| | - S Glass
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC, USA
| | - J Paul
- Cancer Research UK Clinical Trials Unit, Beatson West of Scotland Cancer Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - R Brown
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - A Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - H L McLeod
- Department of Clinical Pharmacology, Xiang-Ya Hospital, Central South University, Changsha, China
- Pharmacogenetics Research institute, Central South University, Changsha, China
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC, USA
- Moffitt Cancer Center, DeBartolo Family Personalized Medicine Institute, Tampa, FL, USA
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Cobb J, Eckhart A, Motsinger-Reif A, Carr B, Groop L, Ferrannini E. α-Hydroxybutyric Acid Is a Selective Metabolite Biomarker of Impaired Glucose Tolerance. Diabetes Care 2016; 39:988-95. [PMID: 27208342 DOI: 10.2337/dc15-2752] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/23/2016] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Plasma metabolites that distinguish isolated impaired glucose tolerance (iIGT) from isolated impaired fasting glucose (iIFG) may be useful biomarkers to predict IGT, a high-risk state for the development of type 2 diabetes. RESEARCH DESIGN AND METHODS Targeted metabolomics with 23 metabolites previously associated with dysglycemia was performed with fasting plasma samples from subjects without diabetes at time 0 of an oral glucose tolerance test (OGTT) in two observational cohorts: RISC (Relationship Between Insulin Sensitivity and Cardiovascular Disease) and DMVhi (Diabetes Mellitus and Vascular Health Initiative). Odds ratios (ORs) for a one-SD change in the metabolite level were calculated using multiple logistic regression models controlling for age, sex, and BMI to test for associations with iIGT or iIFG versus normal. Selective biomarkers of iIGT were further validated in the Botnia study. RESULTS α-Hydroxybutyric acid (α-HB) was most strongly associated with iIGT in RISC (OR 2.54 [95% CI 1.86-3.48], P value 5E-9) and DMVhi (2.75 [1.81-4.19], 4E-5) while having no significant association with iIFG. In Botnia, α-HB was selectively associated with iIGT (2.03 [1.65-2.49], 3E-11) and had no significant association with iIFG. Linoleoyl-glycerophosphocholine (L-GPC) and oleic acid were also found to be selective biomarkers of iIGT. In multivariate IGT prediction models, addition of α-HB, L-GPC, and oleic acid to age, sex, BMI, and fasting glucose significantly improved area under the curve in all three cohorts. CONCLUSIONS α-HB, L-GPC, and oleic acid were shown to be selective biomarkers of iIGT, independent of age, sex, BMI, and fasting glucose, in 4,053 subjects without diabetes from three European cohorts. These biomarkers can be used in predictive models to identify subjects with IGT without performing an OGTT.
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Affiliation(s)
| | | | - Alison Motsinger-Reif
- Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh, NC
| | | | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
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Mochizuki H, Motsinger-Reif A, Bettini C, Moroff S, Breen M. Association of breed and histopathological grade in canine mast cell tumours. Vet Comp Oncol 2016; 15:829-839. [PMID: 27198171 DOI: 10.1111/vco.12225] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 01/25/2023]
Abstract
The aim of this study was to evaluate the relationship between breed and the histopathological grade of canine mast cell tumours (MCTs). A retrospective survey of pathology data of 9375 histopathologically confirmed diagnoses of cutaneous MCTs in the US was evaluated in the context of breed prevalence in over two million registered purebred dogs. Association of histopathological grade with breed, age, sex and spay/neuter status was assessed. The data indicate that the proportion of high-grade tumours increases with advancing age, and that male and intact dogs have increased odds of developing high-grade tumours. A significant difference in the proportion of high-grade tumours between breeds was detected. The Pug was at significantly increased risk of developing low/intermediate-grade tumours, but not high-grade tumours, resulting in preponderance of less aggressive MCTs in this breed. The results of this study suggest a genetic association for the development of high-grade MCTs.
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Affiliation(s)
- H Mochizuki
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - A Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - C Bettini
- American Kennel Club, Raleigh, NC, USA
| | - S Moroff
- Antech Diagnostics Inc., New Hyde Park, NY, USA
| | - M Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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Rotroff D, Breen M, Motsinger-Reif A. Abstract LB-177: Novel approaches for improving interpretation and predictive models of comparative genomic hybridization data. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
As costs of genome wide analyses decline and become more accessible, their use in both human and animal cancer studies are generating increasing information regarding underlying cancer etiology. Comparative genomic hybridization (CGH) is providing valuable information relating copy number aberrations (CNAs) to cancer mechanisms and clinical outcomes. However, challenges exist to interpreting and fully utilizing these data. First, without matched tumor and healthy tissue samples from individuals, distinguishing naturally occurring copy number variations (CNVs) from CNAs is difficult. Second, the large search space of genome wide analyses makes finding combinations of CNAs with improved predictive potential compared to single CNAs challenging. Here we provide novel methods to address these challenges associated with CGH data. Many new resources (e.g. The Cancer Genome Atlas (TCGA)), are making large volumes of genomic data publically accessible. However, most datasets do not have matched normal and tumor tissue samples between subjects. We tested matched normal and tissue samples from 30 patients with colorectal, lung, and pancreatic cancer and compared CNVs and CNAs to findings in larger, non-matched samples in TCGA. Even with limited matched samples, this approach allows for the differentiation of CNVs from CNAs discovered in analyses of non-matched samples.
In some cases, combinations of CNAs can provide improved predictive capability compared to any single CNA. However, it is computationally intractable to exhaustively test combinations of CNAs in a genome-wide study. To address this limitation, we use a novel approach for CNA feature reduction that minimizes the variance within CNA segments across subjects, and Random Forest Ensemble Classification. This approach provides CNA combinations with balanced accuracies of 83.5% and 94.9% for distinguishing 52 cases of canine ALL/AML and 71 cases of B-CLL/T-CLL, respectively. These two approaches address frequent limitations in the interpretation CGH data. Better distinguishing CNVs and interrogating CNA combinations, can provide additional information about the role of CNAs in disease mechanisms and improve treatment decisions.
Citation Format: Daniel Rotroff, Matthew Breen, Alison Motsinger-Reif. Novel approaches for improving interpretation and predictive models of comparative genomic hybridization data. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-177. doi:10.1158/1538-7445.AM2015-LB-177
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Roode SC, Rotroff D, Avery AC, Suter SE, Bienzle D, Schiffman JD, Motsinger-Reif A, Breen M. Genome-wide assessment of recurrent genomic imbalances in canine leukemia identifies evolutionarily conserved regions for subtype differentiation. Chromosome Res 2015; 23:681-708. [PMID: 26037708 DOI: 10.1007/s10577-015-9475-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/02/2015] [Accepted: 05/05/2015] [Indexed: 11/30/2022]
Abstract
Leukemia in dogs is a heterogeneous disease with survival ranging from days to years, depending on the subtype. Strides have been made in both human and canine leukemia to improve classification and understanding of pathogenesis through immunophenotyping, yet classification and choosing appropriate therapy remains challenging. In this study, we assessed 123 cases of canine leukemia (28 ALLs, 24 AMLs, 25 B-CLLs, and 46 T-CLLs) using high-resolution oligonucleotide array comparative genomic hybridization (oaCGH) to detect DNA copy number alterations (CNAs). For the first time, such data were used to identify recurrent CNAs and inclusive genes that may be potential drivers of subtype-specific pathogenesis. We performed predictive modeling to identify CNAs that could reliably differentiate acute subtypes (ALL vs. AML) and chronic subtypes (B-CLL vs. T-CLL) and used this model to differentiate cases with up to 83.3 and 95.8 % precision, respectively, based on CNAs at only one to three genomic regions. In addition, CGH datasets for canine and human leukemia were compared to reveal evolutionarily conserved copy number changes between species, including the shared gain of HSA 21q in ALL and ∼25 Mb of shared gain of HSA 12 and loss of HSA 13q14 in CLL. These findings support the use of canine leukemia as a relevant in vivo model for human leukemia and justify the need to further explore the conserved genomic regions of interest for their clinical impact.
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Affiliation(s)
- Sarah C Roode
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - Daniel Rotroff
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Anne C Avery
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO, USA
| | - Steven E Suter
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA.,Cancer Genetics Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Dorothee Bienzle
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Joshua D Schiffman
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, Center for Children's Cancer Research, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA. .,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA. .,Cancer Genetics Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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Poorman K, Borst L, Moroff S, Roy S, Labelle P, Motsinger-Reif A, Breen M. Comparative cytogenetic characterization of primary canine melanocytic lesions using array CGH and fluorescence in situ hybridization. Chromosome Res 2015; 23:171-86. [PMID: 25511566 PMCID: PMC5462112 DOI: 10.1007/s10577-014-9444-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/07/2014] [Accepted: 10/14/2014] [Indexed: 02/03/2023]
Abstract
Melanocytic lesions originating from the oral mucosa or cutaneous epithelium are common in the general dog population, with up to 100,000 diagnoses each year in the USA. Oral melanoma is the most frequent canine neoplasm of the oral cavity, exhibiting a highly aggressive course. Cutaneous melanocytomas occur frequently, but rarely develop into a malignant form. Despite the differential prognosis, it has been assumed that subtypes of melanocytic lesions represent the same disease. To address the relative paucity of information about their genomic status, molecular cytogenetic analysis was performed on the three recognized subtypes of canine melanocytic lesions. Using array comparative genomic hybridization (aCGH) analysis, highly aberrant distinct copy number status across the tumor genome for both of the malignant melanoma subtypes was revealed. The most frequent aberrations included gain of dog chromosome (CFA) 13 and 17 and loss of CFA 22. Melanocytomas possessed fewer genome wide aberrations, yet showed a recurrent gain of CFA 20q15.3-17. A distinctive copy number profile, evident only in oral melanomas, displayed a sigmoidal pattern of copy number loss followed immediately by a gain, around CFA 30q14. Moreover, when assessed by fluorescence in situ hybridization (FISH), copy number aberrations of targeted genes, such as gain of c-MYC (80 % of cases) and loss of CDKN2A (68 % of cases), were observed. This study suggests that in concordance with what is known for human melanomas, canine melanomas of the oral mucosa and cutaneous epithelium are discrete and initiated by different molecular pathways.
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Affiliation(s)
- Kelsey Poorman
- Department of Molecular Biomedical Science, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
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Knazovicky D, Tomas A, Motsinger-Reif A, Lascelles BDX. Initial evaluation of nighttime restlessness in a naturally occurring canine model of osteoarthritis pain. PeerJ 2015; 3:e772. [PMID: 25722957 PMCID: PMC4340376 DOI: 10.7717/peerj.772] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/26/2015] [Indexed: 12/18/2022] Open
Abstract
Chronic pain due to osteoarthritis (OA) can lead to significant disruption of sleep and increased restlessness. Our objective was to assess whether naturally occurring canine OA is associated with nighttime restlessness and so has potential as a model of OA-associated sleep disturbance. The study was designed as a two-part prospective masked, placebo-controlled study using client-owned dogs (Part A n = 60; Part B n = 19). Inclusion criteria consisted of OA-associated joint pain and mobility impairment. The primary outcome measure for both parts was nighttime accelerometry. In Part B, quality of sleep was assessed using a clinical metrology instrument (Sleep and Night Time Restlessness Evaluation Score, SNoRE). Part A included dogs receiving two weeks of non-steroidal anti-inflammatory drug (NSAID) preceded with two weeks of no treatment. Part B was a crossover study, with NSAID/placebo administered for two weeks followed by a washout period of one week and another two weeks of NSAID/placebo. Repeated measures analysis of variance was used to assess differences between baseline and treatment. There were no significant changes in accelerometry-measured nighttime activity as a result of NSAID administration. SNoRE measures indicated significant improvements in aspects of the quality of nighttime sleep that did not involve obvious movement. These results reflect the few similar studies in human OA patients. Although accelerometry does not appear to be useful, this model has potential to model the human pain-related nighttime sleep disturbance, and other outcome measures should be explored in this model.
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Affiliation(s)
- David Knazovicky
- Comparative Pain Research Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University , Raleigh, NC , USA
| | - Andrea Tomas
- Comparative Pain Research Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University , Raleigh, NC , USA
| | - Alison Motsinger-Reif
- Center for Comparative Medicine and Translational Research, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University , Raleigh, NC , USA ; NCSU Bioinformatics Research Center, Department of Statistics, North Carolina State University , Raleigh, NC , USA
| | - B Duncan X Lascelles
- Comparative Pain Research Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University , Raleigh, NC , USA ; Center for Comparative Medicine and Translational Research, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University , Raleigh, NC , USA ; Center for Pain Research and Innovation, UNC School of Dentistry , Chapel Hill, NC , USA
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Beam AL, Motsinger-Reif A, Doyle J. Bayesian neural networks for detecting epistasis in genetic association studies. BMC Bioinformatics 2014; 15:368. [PMID: 25413600 PMCID: PMC4256933 DOI: 10.1186/s12859-014-0368-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/30/2014] [Indexed: 12/02/2022] Open
Abstract
Background Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. Results A non-parametric Bayesian approach in the form of a Bayesian neural network is proposed for use in analyzing genetic association studies. Demonstrations on synthetic and real data reveal they are able to efficiently and accurately determine which variants are involved in determining case-control status. By using graphics processing units (GPUs) the time needed to build these models is decreased by several orders of magnitude. In comparison with commonly used approaches for detecting interactions, Bayesian neural networks perform very well across a broad spectrum of possible genetic relationships. Conclusions The proposed framework is shown to be a powerful method for detecting causal SNPs while being computationally efficient enough to handle large datasets. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0368-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew L Beam
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA. .,Department of Statistics, North Carolina State University, Raleigh, NC, USA.
| | - Jon Doyle
- Department of Computer Science, North Carolina State University, Raleigh, NC, USA.
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LeVine DN, Birkenheuer AJ, Brooks MB, Nordone SK, Bellinger DA, Jones SL, Fischer TH, Oglesbee SE, Frey K, Brinson NS, Peters AP, Marr HS, Motsinger-Reif A, Gudbrandsdottir S, Bussel JB, Key NS. A novel canine model of immune thrombocytopenia: has immune thrombocytopenia (ITP) gone to the dogs? Br J Haematol 2014; 167:110-20. [PMID: 25039744 DOI: 10.1111/bjh.13005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 05/11/2014] [Indexed: 01/25/2023]
Abstract
Canine immune thrombocytopenia (ITP) is analogous to human ITP, with similar platelet counts and heterogeneity in bleeding phenotype among affected individuals. With a goal of ultimately investigating this bleeding heterogeneity, a canine model of antibody-mediated ITP was developed. Infusion of healthy dogs with 2F9, a murine IgG2a monoclonal antibody to the canine platelet glycoprotein GPIIb (a common target of autoantibodies in ITP) resulted in profound, dose-dependent thrombocytopenia. Model dogs developed variable bleeding phenotypes, e.g. petechiae and haematuria, despite similar degrees of thrombocytopenia. 2F9 infusion was not associated with systemic inflammation, consumptive coagulopathy, or impairment of platelet function. Unexpectedly however, evaluation of cytokine profiles led to the identification of platelets as a potential source of serum interleukin-8 (IL8) in dogs. This finding was confirmed in humans with ITP, suggesting that platelet IL8 may be a previously unrecognized modulator of platelet-neutrophil crosstalk. The utility of this model will allow future study of bleeding phenotypic heterogeneity including the role of neutrophils and endothelial cells in ITP.
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Affiliation(s)
- Dana N LeVine
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA; Department of Pathology and Laboratory Animal Medicine, University of North Carolina, Chapel Hill, NC, USA
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