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James EA, Holers VM, Iyer R, Prideaux EB, Rao NL, Rims C, Muir VS, Posso SE, Bloom MS, Zia A, Elliott SE, Adamska JZ, Ai R, Brewer RC, Seifert JA, Moss L, Barzideh S, Demoruelle MK, Striebich CC, Okamoto Y, Sainbayar E, Crook AA, Peterson RA, Vanderlinden LA, Wang W, Boyle DL, Robinson WH, Buckner JH, Firestein GS, Deane KD. Multifaceted immune dysregulation characterizes individuals at-risk for rheumatoid arthritis. Nat Commun 2023; 14:7637. [PMID: 37993439 PMCID: PMC10665556 DOI: 10.1038/s41467-023-43091-8] [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] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
Molecular markers of autoimmunity, such as antibodies to citrullinated protein antigens (ACPA), are detectable prior to inflammatory arthritis (IA) in rheumatoid arthritis (RA) and may define a state that is 'at-risk' for future RA. Here we present a cross-sectional comparative analysis among three groups that include ACPA positive individuals without IA (At-Risk), ACPA negative individuals and individuals with early, ACPA positive clinical RA (Early RA). Differential methylation analysis among the groups identifies non-specific dysregulation in peripheral B, memory and naïve T cells in At-Risk participants, with more specific immunological pathway abnormalities in Early RA. Tetramer studies show increased abundance of T cells recognizing citrullinated (cit) epitopes in At-Risk participants, including expansion of T cells reactive to citrullinated cartilage intermediate layer protein I (cit-CILP); these T cells have Th1, Th17, and T stem cell memory-like phenotypes. Antibody-antigen array analyses show that antibodies targeting cit-clusterin, cit-fibrinogen and cit-histone H4 are elevated in At-Risk and Early RA participants, with the highest levels of antibodies detected in those with Early RA. These findings indicate that an ACPA positive at-risk state is associated with multifaceted immune dysregulation that may represent a potential opportunity for targeted intervention.
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Affiliation(s)
- Eddie A James
- Benaroya Research Institute, Seattle, WA, 98101, USA
| | - V Michael Holers
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Radhika Iyer
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - E Barton Prideaux
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Navin L Rao
- Janssen Research and Development, Spring House, PA, 19477, USA
| | - Cliff Rims
- Benaroya Research Institute, Seattle, WA, 98101, USA
| | | | | | - Michelle S Bloom
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - Amin Zia
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - Serra E Elliott
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - Julia Z Adamska
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - Rizi Ai
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - R Camille Brewer
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - Jennifer A Seifert
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - LauraKay Moss
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Saman Barzideh
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - M Kristen Demoruelle
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Christopher C Striebich
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Yuko Okamoto
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Division of Rheumatology, Department of Internal Medicine, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Enkhtsogt Sainbayar
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Alexandra A Crook
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Ryan A Peterson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Lauren A Vanderlinden
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - David L Boyle
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - William H Robinson
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | | | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Kevin D Deane
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
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Booher WC, Vanderlinden LA, Hall LA, Thomas AL, Evans LM, Saba LM, Ehringer MA. Hippocampal RNA sequencing in mice selectively bred for high and low activity. Genes Brain Behav 2023; 22:e12832. [PMID: 36514243 PMCID: PMC10067415 DOI: 10.1111/gbb.12832] [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] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022]
Abstract
High and Low Activity strains of mice were bidirectionally selected for differences in open-field activity (DeFries et al., 1978, Behavior Genetics, 8: 3-13) and subsequently inbred to use as a genetic model for studying anxiety-like behaviors (Booher et al., 2021, Genes, Brain and Behavior, 20: e12730). Hippocampal RNA-sequencing of the High and Low Activity mice identified 3901 differentially expressed protein-coding genes, with both sex-dependent and sex-independent effects. Functional enrichment analysis (PANTHER) highlighted 15 gene ontology terms, which allowed us to create a narrow list of 264 top candidate genes. Of the top candidate genes, 46 encoded four Complexes (I, II, IV and V) and two electron carriers (cytochrome c and ubiquinone) of the mitochondrial oxidative phosphorylation process. The most striking results were in the female high anxiety, Low Activity mice, where 39/46 genes relating to oxidative phosphorylation were upregulated. In addition, comparison of our top candidate genes with two previously curated High and Low Activity gene lists highlight 24 overlapping genes, where Ndufa13, which encodes the supernumerary subunit A13 of complex I, was the only gene to be included in all three lists. Mitochondrial dysfunction has recently been implicated as both a cause and effect of anxiety-related disorders and thus should be further explored as a possible novel pharmaceutical treatment for anxiety disorders.
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Affiliation(s)
- Winona C. Booher
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
- Institute for Behavioral GeneticsUniversity of Colorado BoulderBoulderColoradoUSA
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Lauren A. Vanderlinden
- Department of Biostatistics & Informatics, Colorado School of Public HealthUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Lucy A. Hall
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Aimee L. Thomas
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Luke M. Evans
- Institute for Behavioral GeneticsUniversity of Colorado BoulderBoulderColoradoUSA
| | - Laura M. Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Marissa A. Ehringer
- Institute for Behavioral GeneticsUniversity of Colorado BoulderBoulderColoradoUSA
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
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3
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Buckner T, Johnson RK, Vanderlinden LA, Carry PM, Romero A, Onengut-Gumuscu S, Chen WM, Kim S, Fiehn O, Frohnert BI, Crume T, Perng W, Kechris K, Rewers M, Norris JM. Genome-wide analysis of oxylipins and oxylipin profiles in a pediatric population. Front Nutr 2023; 10:1040993. [PMID: 37057071 PMCID: PMC10086335 DOI: 10.3389/fnut.2023.1040993] [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: 09/09/2022] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Background Oxylipins are inflammatory biomarkers derived from omega-3 and-6 fatty acids implicated in inflammatory diseases but have not been studied in a genome-wide association study (GWAS). The aim of this study was to identify genetic loci associated with oxylipins and oxylipin profiles to identify biologic pathways and therapeutic targets for oxylipins. Methods We conducted a GWAS of plasma oxylipins in 316 participants in the Diabetes Autoimmunity Study in the Young (DAISY). DNA samples were genotyped using the TEDDY-T1D Exome array, and additional variants were imputed using the Trans-Omics for Precision Medicine (TOPMed) multi-ancestry reference panel. Principal components analysis of 36 plasma oxylipins was used to capture oxylipin profiles. PC1 represented linoleic acid (LA)- and alpha-linolenic acid (ALA)-related oxylipins, and PC2 represented arachidonic acid (ARA)-related oxylipins. Oxylipin PC1, PC2, and the top five loading oxylipins from each PC were used as outcomes in the GWAS (genome-wide significance: p < 5×10-8). Results The SNP rs143070873 was associated with (p < 5×10-8) the LA-related oxylipin 9-HODE, and rs6444933 (downstream of CLDN11) was associated with the LA-related oxylipin 13 S-HODE. A locus between MIR1302-7 and LOC100131146, rs10118380 and an intronic variant in TRPM3 were associated with the ARA-related oxylipin 11-HETE. These loci are involved in inflammatory signaling cascades and interact with PLA2, an initial step to oxylipin biosynthesis. Conclusion Genetic loci involved in inflammation and oxylipin metabolism are associated with oxylipin levels.
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Affiliation(s)
- Teresa Buckner
- Department of Epidemiology, Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, United States
- Department of Kinesiology, Nutrition, and Dietetics, University of Northern Colorado, Greeley, CO, United States
| | - Randi K. Johnson
- Department of Epidemiology, Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, United States
- Department of Biomedical Informatics, CU School of Medicine, Anschutz Medical Campus, Aurora, CO, United States
| | - Lauren A. Vanderlinden
- Department of Epidemiology, Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, United States
| | - Patrick M. Carry
- Department of Epidemiology, Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, United States
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, CU School of Medicine, Anschutz Medical Campus, Aurora, CO, United States
| | - Alex Romero
- Department of Biomedical Informatics, CU School of Medicine, Anschutz Medical Campus, Aurora, CO, United States
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Soojeong Kim
- Department of Health Administration, Dongseo University, Busan, Republic of Korea
| | - Oliver Fiehn
- NIH-West Coast Metabolomics Center, University of California-Davis, Davis, CA, United States
| | - Brigitte I. Frohnert
- The Barbara Davis Center for Diabetes, CU School of Medicine, Anschutz Medical Campus, Aurora, CO, United States
| | - Tessa Crume
- Department of Epidemiology, Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, United States
| | - Wei Perng
- Department of Epidemiology, Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, United States
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, United States
| | - Marian Rewers
- The Barbara Davis Center for Diabetes, CU School of Medicine, Anschutz Medical Campus, Aurora, CO, United States
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, United States
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4
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Carry PM, Vigers T, Vanderlinden LA, Keeter C, Dong F, Buckner T, Litkowski E, Yang I, Norris JM, Kechris K. Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments. BMC Bioinformatics 2023; 24:86. [PMID: 36882691 PMCID: PMC9990331 DOI: 10.1186/s12859-023-05202-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND We developed a novel approach to minimize batch effects when assigning samples to batches. Our algorithm selects a batch allocation, among all possible ways of assigning samples to batches, that minimizes differences in average propensity score between batches. This strategy was compared to randomization and stratified randomization in a case-control study (30 per group) with a covariate (case vs control, represented as β1, set to be null) and two biologically relevant confounding variables (age, represented as β2, and hemoglobin A1c (HbA1c), represented as β3). Gene expression values were obtained from a publicly available dataset of expression data obtained from pancreas islet cells. Batch effects were simulated as twice the median biological variation across the gene expression dataset and were added to the publicly available dataset to simulate a batch effect condition. Bias was calculated as the absolute difference between observed betas under the batch allocation strategies and the true beta (no batch effects). Bias was also evaluated after adjustment for batch effects using ComBat as well as a linear regression model. In order to understand performance of our optimal allocation strategy under the alternative hypothesis, we also evaluated bias at a single gene associated with both age and HbA1c levels in the 'true' dataset (CAPN13 gene). RESULTS Pre-batch correction, under the null hypothesis (β1), maximum absolute bias and root mean square (RMS) of maximum absolute bias, were minimized using the optimal allocation strategy. Under the alternative hypothesis (β2 and β3 for the CAPN13 gene), maximum absolute bias and RMS of maximum absolute bias were also consistently lower using the optimal allocation strategy. ComBat and the regression batch adjustment methods performed well as the bias estimates moved towards the true values in all conditions under both the null and alternative hypotheses. Although the differences between methods were less pronounced following batch correction, estimates of bias (average and RMS) were consistently lower using the optimal allocation strategy under both the null and alternative hypotheses. CONCLUSIONS Our algorithm provides an extremely flexible and effective method for assigning samples to batches by exploiting knowledge of covariates prior to sample allocation.
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Affiliation(s)
- Patrick M Carry
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado Anschutz Medical Campus, 12631 E. 17Th Ave, Room 4602, Mail Stop B202, Aurora, CO, 80045, USA. .,Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA.
| | - Tim Vigers
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA.,Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lauren A Vanderlinden
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA.,Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Carson Keeter
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado Anschutz Medical Campus, 12631 E. 17Th Ave, Room 4602, Mail Stop B202, Aurora, CO, 80045, USA
| | - Fran Dong
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Teresa Buckner
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - Elizabeth Litkowski
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - Ivana Yang
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
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5
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Buckner T, Johnson RK, Vanderlinden LA, Carry PM, Romero A, Onengut-Gumuscu S, Chen WM, Fiehn O, Frohnert BI, Crume T, Perng W, Kechris K, Rewers M, Norris JM. An Oxylipin-Related Nutrient Pattern and Risk of Type 1 Diabetes in the Diabetes Autoimmunity Study in the Young (DAISY). Nutrients 2023; 15:945. [PMID: 36839302 PMCID: PMC9962656 DOI: 10.3390/nu15040945] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Oxylipins, pro-inflammatory and pro-resolving lipid mediators, are associated with the risk of type 1 diabetes (T1D) and may be influenced by diet. This study aimed to develop a nutrient pattern related to oxylipin profiles and test their associations with the risk of T1D among youth. The nutrient patterns were developed with a reduced rank regression in a nested case-control study (n = 335) within the Diabetes Autoimmunity Study in the Young (DAISY), a longitudinal cohort of children at risk of T1D. The oxylipin profiles (adjusted for genetic predictors) were the response variables. The nutrient patterns were tested in the case-control study (n = 69 T1D cases, 69 controls), then validated in the DAISY cohort using a joint Cox proportional hazards model (n = 1933, including 81 T1D cases). The first nutrient pattern (NP1) was characterized by low beta cryptoxanthin, flavanone, vitamin C, total sugars and iron, and high lycopene, anthocyanidins, linoleic acid and sodium. After adjusting for T1D family history, the HLA genotype, sex and race/ethnicity, NP1 was associated with a lower risk of T1D in the nested case-control study (OR: 0.44, p = 0.0126). NP1 was not associated with the risk of T1D (HR: 0.54, p-value = 0.1829) in the full DAISY cohort. Future studies are needed to confirm the nested case-control findings and investigate the modifiable factors for oxylipins.
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Affiliation(s)
- Teresa Buckner
- Department of Epidemiology, Colorado School of Public Health, CU Anschutz, Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Kinesiology, Nutrition, and Dietetics, University of Northern Colorado, Greeley, CO 80639, USA
| | - Randi K. Johnson
- Department of Epidemiology, Colorado School of Public Health, CU Anschutz, Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biomedical Informatics, CU School of Medicine, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lauren A. Vanderlinden
- Department of Epidemiology, Colorado School of Public Health, CU Anschutz, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Patrick M. Carry
- Department of Epidemiology, Colorado School of Public Health, CU Anschutz, Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, CU School of Medicine, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Alex Romero
- Department of Biomedical Informatics, CU School of Medicine, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Suna Onengut-Gumuscu
- Health Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Wei-Min Chen
- Health Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Oliver Fiehn
- NIH-West Coast Metabolomics Center, University of California-Davis, Davis, CA 95616, USA
| | - Brigitte I. Frohnert
- Department of Epidemiology, Colorado School of Public Health, CU Anschutz, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tessa Crume
- Department of Epidemiology, Colorado School of Public Health, CU Anschutz, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Wei Perng
- Department of Epidemiology, Colorado School of Public Health, CU Anschutz, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Katerina Kechris
- Department of Epidemiology, Colorado School of Public Health, CU Anschutz, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Marian Rewers
- Department of Epidemiology, Colorado School of Public Health, CU Anschutz, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, CU Anschutz, Anschutz Medical Campus, Aurora, CO 80045, USA
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6
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Brice AN, Vanderlinden LA, Marker KM, Mayer D, Lin M, Rafaels N, Shortt JA, Romero A, Lowery JT, Gignoux CR, Johnson RK. COVID-19 Mortality in the Colorado Center for Personalized Medicine Biobank. Int J Environ Res Public Health 2023; 20:2368. [PMID: 36767733 PMCID: PMC9916246 DOI: 10.3390/ijerph20032368] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Over 6.37 million people have died from COVID-19 worldwide, but factors influencing COVID-19-related mortality remain understudied. We aimed to describe and identify risk factors for COVID-19 mortality in the Colorado Center for Personalized Medicine (CCPM) Biobank using integrated data sources, including Electronic Health Records (EHRs). We calculated cause-specific mortality and case-fatality rates for COVID-19 and common pre-existing health conditions defined by diagnostic phecodes and encounters in EHRs. We performed multivariable logistic regression analyses of the association between each pre-existing condition and COVID-19 mortality. Of the 155,859 Biobank participants enrolled as of July 2022, 20,797 had been diagnosed with COVID-19. Of 5334 Biobank participants who had died, 190 were attributed to COVID-19. The case-fatality rate was 0.91% and the COVID-19 mortality rate was 122 per 100,000 persons. The odds of dying from COVID-19 were significantly increased among older men, and those with 14 of the 61 pre-existing conditions tested, including hypertensive chronic kidney disease (OR: 10.14, 95% CI: 5.48, 19.16) and type 2 diabetes with renal manifestations (OR: 5.59, 95% CI: 3.42, 8.97). Male patients who are older and have pre-existing kidney diseases may be at higher risk for death from COVID-19 and may require special care.
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Affiliation(s)
- Amanda N. Brice
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA
| | | | - Katie M. Marker
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David Mayer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, Aurora, CO 80045, USA
| | - Meng Lin
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, Aurora, CO 80045, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, Aurora, CO 80045, USA
| | - Jonathan A. Shortt
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, Aurora, CO 80045, USA
| | - Alex Romero
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jan T. Lowery
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, Aurora, CO 80045, USA
| | - Christopher R. Gignoux
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, Aurora, CO 80045, USA
| | - Randi K. Johnson
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, Aurora, CO 80045, USA
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Pattee J, Vanderlinden LA, Mahaffey S, Hoffman P, Tabakoff B, Saba LM. Evaluation and characterization of expression quantitative trait analysis methods in the Hybrid Rat Diversity Panel. Front Genet 2022; 13:947423. [PMID: 36186443 PMCID: PMC9515987 DOI: 10.3389/fgene.2022.947423] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/26/2022] [Indexed: 01/07/2023] Open
Abstract
The Hybrid Rat Diversity Panel (HRDP) is a stable and well-characterized set of more than 90 inbred rat strains that can be leveraged for systems genetics approaches to understanding the genetic and genomic variation associated with complex disease. The HRDP exhibits substantial between-strain diversity while retaining substantial within-strain isogenicity, allowing for the precise mapping of genetic variation associated with complex phenotypes and providing statistical power to identify associated variants. In order to robustly identify associated genetic variants, it is important to account for the population structure induced by inbreeding. To this end, we investigate the performance of four plausible approaches towards modeling quantitative traits in the HRDP and quantify their operating characteristics. In particular, we investigate three approaches based on genome-wide mixed model analysis, and one approach based on ordinary least squares linear regression. Towards facilitating study planning and design, we conduct extensive simulations to investigate the power of genetic association analyses in the HRDP, and characterize the impressive attained power. In simulation of eQTL data in the HRDP, we find that a mixed model approach that leverages leave-one-chromosome-out kinship estimation attains the highest power while controlling type I error.
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Affiliation(s)
- Jack Pattee
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lauren A. Vanderlinden
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Paula Hoffman
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Laura M. Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,*Correspondence: Laura M. Saba,
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Carry PM, Waugh K, Vanderlinden LA, Johnson RK, Buckner T, Rewers M, Steck AK, Yang I, Fingerlin TE, Kechris K, Norris JM. Changes in the Coexpression of Innate Immunity Genes During Persistent Islet Autoimmunity Are Associated With Progression of Islet Autoimmunity: Diabetes Autoimmunity Study in the Young (DAISY). Diabetes 2022; 71:2048-2057. [PMID: 35724268 PMCID: PMC9450568 DOI: 10.2337/db21-1111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/08/2022] [Indexed: 11/13/2022]
Abstract
Longitudinal changes in gene expression during islet autoimmunity (IA) may provide insight into biological processes that explain progression to type 1 diabetes (T1D). We identified individuals from Diabetes Autoimmunity Study in the Young (DAISY) who developed IA, autoantibodies present on two or more visits. Illumina's NovaSeq 6000 was used to quantify gene expression in whole blood. With linear mixed models we tested for changes in expression after IA that differed across individuals who progressed to T1D (progressors) (n = 25), reverted to an autoantibody-negative stage (reverters) (n = 47), or maintained IA positivity but did not develop T1D (maintainers) (n = 66). Weighted gene coexpression network analysis was used to identify coexpression modules. Gene Ontology pathway analysis of the top 150 differentially expressed genes (nominal P < 0.01) identified significantly enriched pathways including leukocyte activation involved in immune response, innate immune response, and regulation of immune response. We identified a module of 14 coexpressed genes with roles in the innate immunity. The hub gene, LTF, is known to have immunomodulatory properties. Another gene within the module, CAMP, is potentially relevant based on its role in promoting β-cell survival in a murine model. Overall, results provide evidence of alterations in expression of innate immune genes prior to onset of T1D.
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Affiliation(s)
- Patrick M. Carry
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO
| | - Kathleen Waugh
- Barbara Davis Center, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | | | - Randi K. Johnson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Teresa Buckner
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO
| | - Marian Rewers
- Barbara Davis Center, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Andrea K. Steck
- Barbara Davis Center, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ivana Yang
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Tasha E. Fingerlin
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO
| | | | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO
- Barbara Davis Center, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
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Sompel K, Dwyer-Nield LD, Smith AJ, Elango AP, Vanderlinden LA, Kopf K, Keith RL, Tennis MA. Loss of Frizzled 9 in Lung Cells Alters Epithelial Phenotype and Promotes Premalignant Lesion Development. Front Oncol 2022; 12:815737. [PMID: 35924166 PMCID: PMC9343062 DOI: 10.3389/fonc.2022.815737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 06/21/2022] [Indexed: 11/23/2022] Open
Abstract
The transmembrane receptor Frizzled 9 (FZD9) is important for fetal neurologic and bone development through both canonical and non-canonical WNT/FZD signaling. In the adult lung, however, Fzd9 helps to maintain a normal epithelium by signaling through peroxisome proliferator activated receptor γ (PPARγ). The effect of FZD9 loss on normal lung epithelial cells and regulators of its expression in the lung are unknown. We knocked down FZD9 in human bronchial epithelial cell (HBEC) lines and found that downstream EMT targets and PPARγ activity are altered. We used a FZD9-/- mouse in the urethane lung adenocarcinoma model and found FZD9-/- adenomas had more proliferation, increased EMT signaling, decreased activation of PPARγ, increased expression of lung cancer associated genes, increased transformed growth, and increased potential for invasive behavior. We identified PPARγ as a transcriptional regulator of FZD9. We also demonstrated that extended cigarette smoke exposure in HBEC leads to decreased FZD9 expression, decreased activation of PPARγ, and increased transformed growth, and found that higher exposure to cigarette smoke in human lungs leads to decreased FZD9 expression. These results provide evidence for the role of FZD9 in lung epithelial maintenance and in smoking related malignant transformation. We identified the first transcriptional regulator of FZD9 in the lung and found FZD9 negative lesions are more dangerous. Loss of FZD9 creates a permissive environment for development of premalignant lung lesions, making it a potential target for intervention.
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Affiliation(s)
- Kayla Sompel
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lori D Dwyer-Nield
- Skaggs School of Pharmacy, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Alex J Smith
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Alamelu P Elango
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lauren A Vanderlinden
- School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Katrina Kopf
- Office of Academic Affairs, National Jewish Health, Denver, CO, United States
| | - Robert L Keith
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Division of Pulmonary Sciences and Critical Care Medicine, Rocky Mountain Regional Medical Center, Aurora, CO, United States
| | - Meredith A Tennis
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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10
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Vanderlinden LA, Bemis EA, Seifert J, Guthridge JM, Young KA, Demoruelle MK, Feser M, DeJager W, Macwana S, Mikuls TR, O'Dell JR, Weisman MH, Buckner J, Keating RM, Gaffney PM, Kelly JA, Langefeld CD, Deane KD, James JA, Holers VM, Norris JM. Relationship Between a Vitamin D Genetic Risk Score and Autoantibodies Among First-Degree Relatives of Probands With Rheumatoid Arthritis and Systemic Lupus Erythematosus. Front Immunol 2022; 13:881332. [PMID: 35720397 PMCID: PMC9205604 DOI: 10.3389/fimmu.2022.881332] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/09/2022] [Indexed: 12/28/2022] Open
Abstract
Objective Higher 25-hydroxyvitamin D (25(OH)D) levels have been associated with reduced risk for autoimmune diseases and are influenced by vitamin D metabolism genes. We estimated genetically-determined vitamin D levels by calculating a genetic risk score (GRS) and investigated whether the vitamin D GRS was associated with the presence of autoantibodies related to rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) in those at increased risk for developing RA and SLE, respectively. Methods In this cross-sectional study, we selected autoantibody positive (aAb+) and autoantibody negative (aAb-) individuals from the Studies of the Etiologies of Rheumatoid Arthritis (SERA), a cohort study of first-degree relatives (FDRs) of individuals with RA (189 RA aAb+, 181 RA aAb-), and the Lupus Family Registry and Repository (LFRR), a cohort study of FDRs of individuals with SLE (157 SLE aAb+, 185 SLE aAb-). Five SNPs known to be associated with serum 25(OH)D levels were analyzed individually as well as in a GRS: rs4588 (GC), rs12785878 (NADSYN1), rs10741657 (CYP2R1), rs6538691 (AMDHD1), and rs8018720 (SEC23A). Results Both cohorts had similar demographic characteristics, with significantly older and a higher proportion of males in the aAb+ FDRs. The vitamin D GRS was inversely associated with RA aAb+ (OR = 0.85, 95% CI = 0.74-0.99), suggesting a possible protective factor for RA aAb positivity in FDRs of RA probands. The vitamin D GRS was not associated with SLE aAb+ in the LFRR (OR = 1.09, 95% CI = 0.94-1.27). The SEC23A SNP was associated with RA aAb+ in SERA (OR = 0.65, 95% CI = 0.43-0.99); this SNP was not associated with SLE aAb+ in LFRR (OR = 1.41, 95% CI = 0.90 - 2.19). Conclusion Genes associated with vitamin D levels may play a protective role in the development of RA aAbs in FDRs of RA probands, perhaps through affecting lifelong vitamin D status. The GRS and the SEC23A SNP may be of interest for future investigation in pre-clinical RA. In contrast, these results do not support a similar association in SLE FDRs, suggesting other mechanisms involved in the relationship between vitamin D and SLE aAbs not assessed in this study.
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Affiliation(s)
- Lauren A Vanderlinden
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Elizabeth A Bemis
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jennifer Seifert
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Joel M Guthridge
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Kendra A Young
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Mary Kristen Demoruelle
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Marie Feser
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Wade DeJager
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Susan Macwana
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Ted R Mikuls
- Division of Rheumatology and Immunology, University of Nebraska Medical Center and VA Nebraska-Western Iowa Health Care System, Omaha, NE, United States
| | - James R O'Dell
- Division of Rheumatology and Immunology, University of Nebraska Medical Center and VA Nebraska-Western Iowa Health Care System, Omaha, NE, United States
| | - Michael H Weisman
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jane Buckner
- Center for Translational Immunology, Benaroya Research Institute (BRI) at Virginia Mason, Seattle, WA, United States
| | - Richard M Keating
- Division of Rheumatology, Scripps Health, La Jolla, CA, United States
| | - Patrick M Gaffney
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Jennifer A Kelly
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston Salem, NC, United States.,Center for Precision Medicine, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Kevin D Deane
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Judith A James
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Vernon Michael Holers
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jill M Norris
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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11
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Vanderlinden LA, Johnson RK, Carry PM, Dong F, DeMeo DL, Yang IV, Norris JM, Kechris K. An effective processing pipeline for harmonizing DNA methylation data from Illumina's 450K and EPIC platforms for epidemiological studies. BMC Res Notes 2021; 14:352. [PMID: 34496950 PMCID: PMC8424820 DOI: 10.1186/s13104-021-05741-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 09/25/2020] [Accepted: 08/16/2021] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE Illumina BeadChip arrays are commonly used to generate DNA methylation data for large epidemiological studies. Updates in technology over time create challenges for data harmonization within and between studies, many of which obtained data from the older 450K and newer EPIC platforms. The pre-processing pipeline for DNA methylation is not trivial, and influences the downstream analyses. Incorporating different platforms adds a new level of technical variability that has not yet been taken into account by recommended pipelines. Our study evaluated the performance of various tools on different versions of platform data harmonization at each step of pre-processing pipeline, including quality control (QC), normalization, batch effect adjustment, and genomic inflation. We illustrate our novel approach using 450K and EPIC data from the Diabetes Autoimmunity Study in the Young (DAISY) prospective cohort. RESULTS We found normalization and probe filtering had the biggest effect on data harmonization. Employing a meta-analysis was an effective and easily executable method for accounting for platform variability. Correcting for genomic inflation also helped with harmonization. We present guidelines for studies seeking to harmonize data from the 450K and EPIC platforms, which includes the use of technical replicates for evaluating numerous pre-processing steps, and employing a meta-analysis.
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Affiliation(s)
- Lauren A Vanderlinden
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Randi K Johnson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Patrick M Carry
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fran Dong
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ivana V Yang
- School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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12
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Vigers T, Vanderlinden LA, Johnson RK, Carry PM, Yang I, DeFelice BC, Kaizer AM, Pyle L, Rewers M, Fiehn O, Norris JM, Kechris K. A Mediation Approach to Discovering Causal Relationships between the Metabolome and DNA Methylation in Type 1 Diabetes. Metabolites 2021; 11:metabo11080542. [PMID: 34436483 PMCID: PMC8399445 DOI: 10.3390/metabo11080542] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
Environmental factors including viruses, diet, and the metabolome have been linked with the appearance of islet autoimmunity (IA) that precedes development of type 1 diabetes (T1D). We measured global DNA methylation (DNAm) and untargeted metabolomics prior to IA and at the time of seroconversion to IA in 92 IA cases and 91 controls from the Diabetes Autoimmunity Study in the Young (DAISY). Causal mediation models were used to identify seven DNAm probe-metabolite pairs in which the metabolite measured at IA mediated the protective effect of the DNAm probe measured prior to IA against IA risk. These pairs included five DNAm probes mediated by histidine (a metabolite known to affect T1D risk), one probe (cg01604946) mediated by phostidyl choline p-32:0 or o-32:1, and one probe (cg00390143) mediated by sphingomyelin d34:2. The top 100 DNAm probes were over-represented in six reactome pathways at the FDR <0.1 level (q = 0.071), including transport of small molecules and inositol phosphate metabolism. While the causal pathways in our mediation models require further investigation to better understand the biological mechanisms, we identified seven methylation sites that may improve our understanding of epigenetic protection against T1D as mediated by the metabolome.
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Affiliation(s)
- Tim Vigers
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, CO 80045, USA; (A.M.K.); (L.P.); (K.K.)
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO 80045, USA; (P.M.C.); (J.M.N.)
- Correspondence:
| | - Lauren A. Vanderlinden
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO 80045, USA; (L.A.V.); (M.R.)
| | - Randi K. Johnson
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Aurora, CO 80045, USA; (R.K.J.); (I.Y.)
| | - Patrick M. Carry
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO 80045, USA; (P.M.C.); (J.M.N.)
| | - Ivana Yang
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Aurora, CO 80045, USA; (R.K.J.); (I.Y.)
| | - Brian C. DeFelice
- West Coast Metabolomics Center, University of California, Davis, CA 95616, USA; (B.C.D.); (O.F.)
| | - Alexander M. Kaizer
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, CO 80045, USA; (A.M.K.); (L.P.); (K.K.)
| | - Laura Pyle
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, CO 80045, USA; (A.M.K.); (L.P.); (K.K.)
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO 80045, USA; (P.M.C.); (J.M.N.)
| | - Marian Rewers
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO 80045, USA; (L.A.V.); (M.R.)
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, CA 95616, USA; (B.C.D.); (O.F.)
| | - Jill M. Norris
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO 80045, USA; (P.M.C.); (J.M.N.)
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO 80045, USA; (L.A.V.); (M.R.)
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, CO 80045, USA; (A.M.K.); (L.P.); (K.K.)
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13
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Buckner T, Vanderlinden LA, DeFelice BC, Carry PM, Kechris K, Dong F, Fiehn O, Frohnert BI, Clare-Salzler M, Rewers M, Norris JM. The oxylipin profile is associated with development of type 1 diabetes: the Diabetes Autoimmunity Study in the Young (DAISY). Diabetologia 2021; 64:1785-1794. [PMID: 33893822 PMCID: PMC8249332 DOI: 10.1007/s00125-021-05457-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/21/2020] [Accepted: 02/24/2021] [Indexed: 12/22/2022]
Abstract
AIMS/HYPOTHESIS Oxylipins are lipid mediators derived from polyunsaturated fatty acids. Some oxylipins are proinflammatory (e.g. those derived from arachidonic acid [ARA]), others are pro-resolving of inflammation (e.g. those derived from α-linolenic acid [ALA], docosahexaenoic acid [DHA] and eicosapentaenoic acid [EPA]) and others may be both (e.g. those derived from linoleic acid [LA]). The goal of this study was to examine whether oxylipins are associated with incident type 1 diabetes. METHODS We conducted a nested case-control analysis in the Diabetes Autoimmunity Study in the Young (DAISY), a prospective cohort study of children at risk of type 1 diabetes. Plasma levels of 14 ARA-derived oxylipins, ten LA-derived oxylipins, six ALA-derived oxylipins, four DHA-derived oxylipins and two EPA-related oxylipins were measured by ultra-HPLC-MS/MS at multiple timepoints related to autoantibody seroconversion in 72 type 1 diabetes cases and 71 control participants, which were frequency matched on age at autoantibody seroconversion (of the case), ethnicity and sample availability. Linear mixed models were used to obtain an age-adjusted mean of each oxylipin prior to type 1 diabetes. Age-adjusted mean oxylipins were tested for association with type 1 diabetes using logistic regression, adjusting for the high risk HLA genotype HLA-DR3/4,DQB1*0302. We also performed principal component analysis of the oxylipins and tested principal components (PCs) for association with type 1 diabetes. Finally, to investigate potential critical timepoints, we examined the association of oxylipins measured before and after autoantibody seroconversion (of the cases) using PCs of the oxylipins at those visits. RESULTS The ARA-related oxylipin 5-HETE was associated with increased type 1 diabetes risk. Five LA-related oxylipins, two ALA-related oxylipins and one DHA-related oxylipin were associated with decreased type 1 diabetes risk. A profile of elevated LA- and ALA-related oxylipins (PC1) was associated with decreased type 1 diabetes risk (OR 0.61; 95% CI 0.40, 0.94). A profile of elevated ARA-related oxylipins (PC2) was associated with increased diabetes risk (OR 1.53; 95% CI 1.03, 2.29). A critical timepoint analysis showed type 1 diabetes was associated with a high ARA-related oxylipin profile at post-autoantibody-seroconversion but not pre-seroconversion. CONCLUSIONS/INTERPRETATION The protective association of higher LA- and ALA-related oxylipins demonstrates the importance of both inflammation promotion and resolution in type 1 diabetes. Proinflammatory ARA-related oxylipins may play an important role once the autoimmune process has begun.
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Affiliation(s)
- Teresa Buckner
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | | | - Patrick M Carry
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Fran Dong
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | | | | | - Marian Rewers
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jill M Norris
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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14
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Carry PM, Vanderlinden LA, Johnson RK, Buckner T, Fiehn O, Steck AK, Kechris K, Yang I, Fingerlin TE, Rewers M, Norris JM. Phospholipid Levels at Seroconversion Are Associated With Resolution of Persistent Islet Autoimmunity: The Diabetes Autoimmunity Study in the Young. Diabetes 2021; 70:1592-1601. [PMID: 33863802 PMCID: PMC8336007 DOI: 10.2337/db20-1251] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/11/2021] [Indexed: 12/14/2022]
Abstract
Reversion of islet autoimmunity (IA) may point to mechanisms that prevent IA progression. We followed 199 individuals who developed IA during the Diabetes Autoimmunity Study in the Young. Untargeted metabolomics was performed in serum samples following IA. Cox proportional hazards models were used to test whether the metabolites (2,487) predicted IA reversion: two or more consecutive visits negative for all autoantibodies. We conducted a principal components analysis (PCA) of the top metabolites; |hazard ratio (HR) >1.25| and nominal P < 0.01. Phosphatidylcholine (16:0_18:1(9Z)) was the strongest individual metabolite (HR per 1 SD 2.16, false discovery rate (FDR)-adjusted P = 0.0037). Enrichment analysis identified four clusters (FDR P < 0.10) characterized by an overabundance of sphingomyelin (d40:0), phosphatidylcholine (16:0_18:1(9Z)), phosphatidylcholine (30:0), and l-decanoylcarnitine. Overall, 63 metabolites met the criteria for inclusion in the PCA. PC1 (HR 1.4, P < 0.0001), PC2 (HR 0.85, P = 0.0185), and PC4 (HR 1.28, P = 0.0103) were associated with IA reversion. Given the potential influence of diet on the metabolome, we investigated whether nutrients were correlated with PCs. We identified 20 nutrients that were correlated with the PCs (P < 0.05). Total sugar intake was the top nutrient. Overall, we identified an association between phosphatidylcholine, sphingomyelin, and carnitine levels and reversion of IA.
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Affiliation(s)
- Patrick M Carry
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO
| | | | - Randi K Johnson
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Teresa Buckner
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO
| | | | - Andrea K Steck
- Barbara Davis Center for Diabetes, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO
| | - Ivana Yang
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Tasha E Fingerlin
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO
| | - Marian Rewers
- Barbara Davis Center for Diabetes, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO
- Barbara Davis Center for Diabetes, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
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15
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Carry PM, Vanderlinden LA, Dong F, Buckner T, Litkowski E, Vigers T, Norris JM, Kechris K. Inverse probability weighting is an effective method to address selection bias during the analysis of high dimensional data. Genet Epidemiol 2021; 45:593-603. [PMID: 34130352 DOI: 10.1002/gepi.22418] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 11/11/2022]
Abstract
Omics studies frequently use samples collected during cohort studies. Conditioning on sample availability can cause selection bias if sample availability is nonrandom. Inverse probability weighting (IPW) is purported to reduce this bias. We evaluated IPW in an epigenome-wide analysis testing the association between DNA methylation (261,435 probes) and age in healthy adolescent subjects (n = 114). We simulated age and sex to be correlated with sample selection and then evaluated four conditions: complete population/no selection bias (all subjects), naïve selection bias (no adjustment), and IPW selection bias (selection bias with IPW adjustment). Assuming the complete population condition represented the "truth," we compared each condition to the complete population condition. Bias or difference in associations between age and methylation was reduced in the IPW condition versus the naïve condition. However, genomic inflation and type 1 error were higher in the IPW condition relative to the naïve condition. Postadjustment using bacon, type 1 error and inflation were similar across all conditions. Power was higher under the IPW condition compared with the naïve condition before and after inflation adjustment. IPW methods can reduce bias in genome-wide analyses. Genomic inflation is a potential concern that can be minimized using methods that adjust for inflation.
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Affiliation(s)
- Patrick M Carry
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA.,Department of Orthopedics, Musculoskeletal Research Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Lauren A Vanderlinden
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA.,Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Fran Dong
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Teresa Buckner
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Elizabeth Litkowski
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Timothy Vigers
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
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16
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Travers JG, Wennersten SA, Peña B, Bagchi RA, Smith HE, Hirsch RA, Vanderlinden LA, Lin YH, Dobrinskikh E, Demos-Davies KM, Cavasin MA, Mestroni L, Steinkühler C, Lin CY, Houser SR, Woulfe KC, Lam MPY, McKinsey TA. HDAC Inhibition Reverses Preexisting Diastolic Dysfunction and Blocks Covert Extracellular Matrix Remodeling. Circulation 2021; 143:1874-1890. [PMID: 33682427 DOI: 10.1161/circulationaha.120.046462] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Diastolic dysfunction (DD) is associated with the development of heart failure and contributes to the pathogenesis of other cardiac maladies, including atrial fibrillation. Inhibition of histone deacetylases (HDACs) has been shown to prevent DD by enhancing myofibril relaxation. We addressed the therapeutic potential of HDAC inhibition in a model of established DD with preserved ejection fraction. METHODS Four weeks after uninephrectomy and implantation with deoxycorticosterone acetate pellets, when DD was clearly evident, 1 cohort of mice was administered the clinical-stage HDAC inhibitor ITF2357/Givinostat. Echocardiography, blood pressure measurements, and end point invasive hemodynamic analyses were performed. Myofibril mechanics and intact cardiomyocyte relaxation were assessed ex vivo. Cardiac fibrosis was evaluated by picrosirius red staining and second harmonic generation microscopy of left ventricle (LV) sections, RNA sequencing of LV mRNA, mass spectrometry-based evaluation of decellularized LV biopsies, and atomic force microscopy determination of LV stiffness. Mechanistic studies were performed with primary rat and human cardiac fibroblasts. RESULTS HDAC inhibition normalized DD without lowering blood pressure in this model of systemic hypertension. In contrast to previous models, myofibril relaxation was unimpaired in uninephrectomy/deoxycorticosterone acetate mice. Furthermore, cardiac fibrosis was not evident in any mouse cohort on the basis of picrosirius red staining or second harmonic generation microscopy. However, mass spectrometry revealed induction in the expression of >100 extracellular matrix proteins in LVs of uninephrectomy/deoxycorticosterone acetate mice, which correlated with profound tissue stiffening based on atomic force microscopy. ITF2357/Givinostat treatment blocked extracellular matrix expansion and LV stiffening. The HDAC inhibitor was subsequently shown to suppress cardiac fibroblast activation, at least in part, by blunting recruitment of the profibrotic chromatin reader protein BRD4 (bromodomain-containing protein 4) to key gene regulatory elements. CONCLUSIONS These findings demonstrate the potential of HDAC inhibition as a therapeutic intervention to reverse existing DD and establish blockade of extracellular matrix remodeling as a second mechanism by which HDAC inhibitors improve ventricular filling. Our data reveal the existence of pathophysiologically relevant covert or hidden cardiac fibrosis that is below the limit of detection of histochemical stains such as picrosirius red, highlighting the need to evaluate fibrosis of the heart using diverse methodologies.
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Affiliation(s)
- Joshua G Travers
- Department of Medicine, Division of Cardiology (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., K.M.D.-D., M.A.C., L.M., K.C.W., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora.,Consortium for Fibrosis Research & Translation (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., M.A.C., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
| | - Sara A Wennersten
- Department of Medicine, Division of Cardiology (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., K.M.D.-D., M.A.C., L.M., K.C.W., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora.,Consortium for Fibrosis Research & Translation (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., M.A.C., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
| | - Brisa Peña
- Department of Medicine, Division of Cardiology (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., K.M.D.-D., M.A.C., L.M., K.C.W., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora.,Consortium for Fibrosis Research & Translation (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., M.A.C., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
| | - Rushita A Bagchi
- Department of Medicine, Division of Cardiology (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., K.M.D.-D., M.A.C., L.M., K.C.W., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora.,Consortium for Fibrosis Research & Translation (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., M.A.C., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
| | - Harrison E Smith
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX (H.E.S., R.A.H., C.Y.L.).,Department of Biostatistics and Informatics (H.E.S., L.A.V.), Colorado School of Public Health, Aurora
| | - Rachel A Hirsch
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX (H.E.S., R.A.H., C.Y.L.)
| | - Lauren A Vanderlinden
- Department of Biostatistics and Informatics (H.E.S., L.A.V.), Colorado School of Public Health, Aurora
| | - Ying-Hsi Lin
- Department of Medicine, Division of Cardiology (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., K.M.D.-D., M.A.C., L.M., K.C.W., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora.,Consortium for Fibrosis Research & Translation (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., M.A.C., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
| | - Evgenia Dobrinskikh
- Department of Medicine, Division of Pulmonary Sciences & Critical Care (E.D.), University of Colorado Anschutz Medical Campus, Aurora
| | - Kimberly M Demos-Davies
- Department of Medicine, Division of Cardiology (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., K.M.D.-D., M.A.C., L.M., K.C.W., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
| | - Maria A Cavasin
- Department of Medicine, Division of Cardiology (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., K.M.D.-D., M.A.C., L.M., K.C.W., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora.,Consortium for Fibrosis Research & Translation (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., M.A.C., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
| | - Luisa Mestroni
- Department of Medicine, Division of Cardiology (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., K.M.D.-D., M.A.C., L.M., K.C.W., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
| | | | - Charles Y Lin
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX (H.E.S., R.A.H., C.Y.L.).,now with Kronos Bio, Cambridge, MA (C.Y.L.)
| | - Steven R Houser
- Cardiovascular Research Center (S.R.H.), Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Kathleen C Woulfe
- Department of Medicine, Division of Cardiology (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., K.M.D.-D., M.A.C., L.M., K.C.W., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
| | - Maggie P Y Lam
- Department of Medicine, Division of Cardiology (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., K.M.D.-D., M.A.C., L.M., K.C.W., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora.,Consortium for Fibrosis Research & Translation (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., M.A.C., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
| | - Timothy A McKinsey
- Department of Medicine, Division of Cardiology (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., K.M.D.-D., M.A.C., L.M., K.C.W., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora.,Consortium for Fibrosis Research & Translation (J.G.T., S.A.W., B.P., R.A.B., Y.-H.L., M.A.C., M.P.Y.L., T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
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17
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Johnson RK, Vanderlinden LA, DeFelice BC, Uusitalo U, Seifert J, Fan S, Crume T, Fiehn O, Rewers M, Kechris K, Norris JM. Metabolomics-related nutrient patterns at seroconversion and risk of progression to type 1 diabetes. Pediatr Diabetes 2020; 21:1202-1209. [PMID: 32686271 PMCID: PMC7855902 DOI: 10.1111/pedi.13085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/11/2020] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Our aim was to elucidate the role of diet in type 1 diabetes (T1D) by examining combinations of nutrient intake in the progression from islet autoimmunity (IA) to T1D. METHODS We measured 2457 metabolites and dietary intake at the time of seroconversion in 132 IA-positive children in the prospective Diabetes Autoimmunity Study in the Young. IA was defined as the first of two consecutive visits positive for at least one autoantibody (insulin, GAD, IA-2, or ZnT8). By December 2018, 40 children progressed to T1D. Intakes of 38 nutrients were estimated from semiquantitative food frequency questionnaires. We tested the association of each metabolite with progression to T1D using multivariable Cox regression. Nutrient patterns that best explained variation in candidate metabolites were identified using reduced rank regression (RRR), and their association with progression to T1D was tested using Cox regression adjusting for age at seroconversion and high-risk HLA genotype. RESULTS In stepwise selection, 22 nutrients significantly predicted at least two of the 13 most significant metabolites associated with progression to T1D, and were included in RRR. A nutrient pattern corresponding to intake lower in linoleic acid, niacin, and riboflavin, and higher in total sugars, explained 18% of metabolite variability. Children scoring higher on this metabolite-related nutrient pattern at seroconversion had increased risk for progressing to T1D (HR = 3.17, 95%CI = 1.42-7.05). CONCLUSIONS Combinations of nutrient intake reflecting candidate metabolites are associated with increased risk of T1D, and may help focus dietary prevention efforts.
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Affiliation(s)
- Randi K. Johnson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado,Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Lauren A. Vanderlinden
- Department of Biostatistics & Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Brian C. DeFelice
- UC Davis Genome Center—Metabolomics, University of California Davis, Davis, California
| | - Ulla Uusitalo
- Health Informatics Institute, University of South Florida College of Medicine, Tampa, Florida
| | - Jennifer Seifert
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Sili Fan
- UC Davis Genome Center—Metabolomics, University of California Davis, Davis, California
| | - Tessa Crume
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Oliver Fiehn
- UC Davis Genome Center—Metabolomics, University of California Davis, Davis, California
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Katerina Kechris
- Department of Biostatistics & Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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18
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Venter C, Agostoni C, Arshad SH, Ben-Abdallah M, Du Toit G, Fleischer DM, Greenhawt M, Glueck DH, Groetch M, Lunjani N, Maslin K, Maiorella A, Meyer R, Antonella M, Netting MJ, Ibeabughichi Nwaru B, Palmer DJ, Palumbo MP, Roberts G, Roduit C, Smith P, Untersmayr E, Vanderlinden LA, O'Mahony L. Dietary factors during pregnancy and atopic outcomes in childhood: A systematic review from the European Academy of Allergy and Clinical Immunology. Pediatr Allergy Immunol 2020; 31:889-912. [PMID: 32524677 PMCID: PMC9588404 DOI: 10.1111/pai.13303] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/06/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022]
Abstract
RATIONALE Allergic diseases are an increasing public health concern, and early life environment is critical to immune development. Maternal diet during pregnancy has been linked to offspring allergy risk. In turn, maternal diet is a potentially modifiable factor, which could be targeted as an allergy prevention strategy. In this systematic review, we focused on non-allergen-specific modifying factors of the maternal diet in pregnancy on allergy outcomes in their offspring. METHODS We undertook a systematic review of studies investigating the association between maternal diet during pregnancy and allergic outcomes (asthma/wheeze, hay fever/allergic rhinitis/seasonal allergies, eczema/atopic dermatitis (AD), food allergies, and allergic sensitization) in offspring. Studies evaluating the effect of food allergen intake were excluded. We searched three bibliographic databases (MEDLINE, EMBASE, and Web of Science) through February 26, 2019. Evidence was critically appraised using modified versions of the Cochrane Collaboration Risk of Bias tool for intervention trials and the National Institute for Clinical Excellence methodological checklist for cohort and case-control studies and meta-analysis performed from RCTs. RESULTS We identified 95 papers: 17 RCTs and 78 observational (case-control, cross-sectional, and cohort) studies. Observational studies varied in design and dietary intakes and often had contradictory findings. Based on our meta-analysis, RCTs showed that vitamin D supplementation (OR: 0.72; 95% CI: 0.56-0.92) is associated with a reduced risk of wheeze/asthma. A positive trend for omega-3 fatty acids was observed for asthma/wheeze, but this did not reach statistical significance (OR: 0.70; 95% CI: 0.45-1.08). Omega-3 supplementation was also associated with a non-significant decreased risk of allergic rhinitis (OR: 0.76; 95% CI: 0.56-1.04). Neither vitamin D nor omega-3 fatty acids were associated with an altered risk of AD or food allergy. CONCLUSIONS Prenatal supplementation with vitamin D may have beneficial effects for prevention of asthma. Additional nutritional factors seem to be required for modulating the risk of skin and gastrointestinal outcomes. We found no consistent evidence regarding other dietary factors, perhaps due to differences in study design and host features that were not considered. While confirmatory studies are required, there is also a need for performing RCTs beyond single nutrients/foods.
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Affiliation(s)
- Carina Venter
- Section of Allergy and Immunology, University of Colorado School of Medicine, Denver, CO, USA.,Children's Hospital Colorado, Aurora, CO, USA
| | - Carlo Agostoni
- Pediatria Media Intensità di Cura Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinic, Milan, Italy
| | - S Hasan Arshad
- Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,The David Hide Asthma and Allergy Centre, Isle of Wight, UK
| | | | - George Du Toit
- Department of Paediatric Allergy, Division of Asthma, Allergy and Lung Biology, King's College London, London, UK.,Evelina London, Guy's & St Thomas' Hospital, London, UK
| | - David M Fleischer
- Section of Allergy and Immunology, University of Colorado School of Medicine, Denver, CO, USA.,Children's Hospital Colorado, Aurora, CO, USA
| | - Matthew Greenhawt
- Section of Allergy and Immunology, University of Colorado School of Medicine, Denver, CO, USA.,Children's Hospital Colorado, Aurora, CO, USA
| | - Deborah H Glueck
- Department of Pediatrics, University of Colorado School of Medicine, Denver, CO, USA
| | - Marion Groetch
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nonhlanhla Lunjani
- University of Zurich, Davos, Switzerland.,University of Cape Town, Cape Town, South Africa
| | | | | | | | - Muraro Antonella
- Centro di Specializzazione Regionale per lo Studio e la Cura delle Allergie e delle Intolleranze Alimentari presso l'Azienda Ospedaliera, Università di Padova, Padova, Italy
| | - Merryn J Netting
- Women and Kids Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Discipline of Pediatrics, University of Adelaide, Adelaide, SA, Australia
| | | | - Debra J Palmer
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Micheala P Palumbo
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Colorado School of Public Health, Colorado, USA
| | - Graham Roberts
- The David Hide Asthma and Allergy Centre, Isle of Wight, UK.,Department of Paediatric Allergy, Division of Asthma, Allergy and Lung Biology, King's College London, London, UK.,NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK.,Faculty of Medicine, Human Development in Health Academic Units, University of Southampton, Southampton, UK
| | - Caroline Roduit
- University Children's Hospital Zurich, Switzerland.,Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland
| | - Pete Smith
- School of Medicine, Griffith University, Southport, Australia
| | - Eva Untersmayr
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Lauren A Vanderlinden
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Liam O'Mahony
- Departments of Medicine and Microbiology, APC Microbiome Ireland, National University of Ireland, Cork, Ireland
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19
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Carry PM, Vanderlinden LA, Johnson RK, Dong F, Steck AK, Frohnert BI, Rewers M, Yang IV, Kechris K, Norris JM. DNA methylation near the INS gene is associated with INS genetic variation (rs689) and type 1 diabetes in the Diabetes Autoimmunity Study in the Young. Pediatr Diabetes 2020; 21:597-605. [PMID: 32061050 PMCID: PMC7378362 DOI: 10.1111/pedi.12995] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE Mechanisms underlying the role of non-human leukocyte antigen (HLA) genetic risk variants in type 1 diabetes (T1D) are poorly understood. We aimed to test the association between methylation and non-HLA genetic risk. METHODS We conducted a methylation quantitative trait loci (mQTL) analysis in a nested case-control study from the Dietary Autoimmunity Study in the Young. Controls (n = 83) were frequency-matched to T1D cases (n = 83) based on age, race/ethnicity, and sample availability. We evaluated 13 non-HLA genetic markers known be associated with T1D. Genome-wide methylation profiling was performed on peripheral blood samples collected prior to T1D using the Illumina 450 K (discovery set) and infinium methylation EPIC beadchip (EPIC validation) platforms. Linear regression models, adjusting for age and sex, were used to test to each single nucleotide polymorphism (SNP) -probe combination. Logistic regression models were used to test the association between T1D and methylation levels among probes with a significant mQTL. A meta-analysis was used to combine odds ratios from the two platforms. RESULTS We identified 10 SNP-methylation probe pairs (false discovery rate (FDR) adjusted P < .05 and validation P < .05). Probes were associated with the GSDMB, C1QTNF6, IL27, and INS genes. The cg03366382 (OR: 1.9, meta-P = .0495), cg21574853 (OR: 2.5, meta-P = .0232), and cg25336198 (odds ratio: 6.6, meta-P = .0081) probes were significantly associated with T1D. The three probes were located upstream from the INS transcription start site. CONCLUSIONS We confirmed an association between DNA methylation and rs689 that has been identified in related studies. Measurements in our study preceded the onset of T1D suggesting methylation may have a role in the relationship between INS variation and T1D development.
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Affiliation(s)
- Patrick M. Carry
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Lauren A. Vanderlinden
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Randi K. Johnson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Fran Dong
- Barbara Davis Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Andrea K. Steck
- Barbara Davis Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado,University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado
| | - Brigitte I. Frohnert
- Barbara Davis Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado,University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado
| | - Marian Rewers
- Barbara Davis Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado,University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado
| | - Ivana V. Yang
- University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado
| | - Katerina Kechris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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20
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Johnson RK, Vanderlinden LA, Dong F, Carry PM, Seifert J, Waugh K, Shorrosh H, Fingerlin T, Frohnert BI, Yang IV, Kechris K, Rewers M, Norris JM. Longitudinal DNA methylation differences precede type 1 diabetes. Sci Rep 2020; 10:3721. [PMID: 32111940 PMCID: PMC7048736 DOI: 10.1038/s41598-020-60758-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 10/07/2019] [Accepted: 02/14/2020] [Indexed: 12/26/2022] Open
Abstract
DNA methylation may be involved in development of type 1 diabetes (T1D), but previous epigenome-wide association studies were conducted among cases with clinically diagnosed diabetes. Using multiple pre-disease peripheral blood samples on the Illumina 450 K and EPIC platforms, we investigated longitudinal methylation differences between 87 T1D cases and 87 controls from the prospective Diabetes Autoimmunity Study in the Young (DAISY) cohort. Change in methylation with age differed between cases and controls in 10 regions. Average longitudinal methylation differed between cases and controls at two genomic positions and 28 regions. Some methylation differences were detectable and consistent as early as birth, including before and after the onset of preclinical islet autoimmunity. Results map to transcription factors, other protein coding genes, and non-coding regions of the genome with regulatory potential. The identification of methylation differences that predate islet autoimmunity and clinical diagnosis may suggest a role for epigenetics in T1D pathogenesis; however, functional validation is warranted.
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Affiliation(s)
- Randi K Johnson
- University of Colorado Anschutz Medical Campus, Division of Biomedical Informatics and Personalized Medicine, Aurora, CO, USA
| | - Lauren A Vanderlinden
- Colorado School of Public Health, Department of Biostatistics and Informatics, Aurora, CO, USA
| | - Fran Dong
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Patrick M Carry
- Colorado School of Public Health, Department of Epidemiology, Aurora, CO, USA
| | - Jennifer Seifert
- Colorado School of Public Health, Department of Epidemiology, Aurora, CO, USA
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hanan Shorrosh
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Brigitte I Frohnert
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ivana V Yang
- University of Colorado Anschutz Medical Campus, Division of Biomedical Informatics and Personalized Medicine, Aurora, CO, USA
| | - Katerina Kechris
- Colorado School of Public Health, Department of Biostatistics and Informatics, Aurora, CO, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jill M Norris
- Colorado School of Public Health, Department of Epidemiology, Aurora, CO, USA.
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21
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Wheeler LJ, Watson ZL, Qamar L, Yamamoto TM, Sawyer BT, Sullivan KD, Khanal S, Joshi M, Ferchaud-Roucher V, Smith H, Vanderlinden LA, Brubaker SW, Caino CM, Kim H, Espinosa JM, Richer JK, Bitler BG. Multi-Omic Approaches Identify Metabolic and Autophagy Regulators Important in Ovarian Cancer Dissemination. iScience 2019; 19:474-491. [PMID: 31437751 PMCID: PMC6710300 DOI: 10.1016/j.isci.2019.07.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/24/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023] Open
Abstract
High-grade serous ovarian cancers (HGSOCs) arise from exfoliation of transformed cells from the fallopian tube, indicating that survival in suspension, and potentially escape from anoikis, is required for dissemination. We report here the results of a multi-omic study to identify drivers of anoikis escape, including transcriptomic analysis, global non-targeted metabolomics, and a genome-wide CRISPR/Cas9 knockout (GeCKO) screen of HGSOC cells cultured in adherent and suspension settings. Our combined approach identified known pathways, including NOTCH signaling, as well as novel regulators of anoikis escape. Newly identified genes include effectors of fatty acid metabolism, ACADVL and ECHDC2, and an autophagy regulator, ULK1. Knockdown of these genes significantly inhibited suspension growth of HGSOC cells, and the metabolic profile confirmed the role of fatty acid metabolism in survival in suspension. Integration of our datasets identified an anoikis-escape gene signature that predicts overall survival in many carcinomas.
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Affiliation(s)
- Lindsay J Wheeler
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Zachary L Watson
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, 12700 E. 19(th) Avenue, MS 8613, Aurora, CO 80045, USA
| | - Lubna Qamar
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, 12700 E. 19(th) Avenue, MS 8613, Aurora, CO 80045, USA
| | - Tomomi M Yamamoto
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, 12700 E. 19(th) Avenue, MS 8613, Aurora, CO 80045, USA
| | - Brandon T Sawyer
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kelly D Sullivan
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Santosh Khanal
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Molishree Joshi
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Veronique Ferchaud-Roucher
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Harry Smith
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lauren A Vanderlinden
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sky W Brubaker
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cecilia M Caino
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Hyunmin Kim
- Translational Bioinformatics and Cancer Systems Biology Laboratory, Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joaquin M Espinosa
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jennifer K Richer
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Benjamin G Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, 12700 E. 19(th) Avenue, MS 8613, Aurora, CO 80045, USA.
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22
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Lusk R, Saba LM, Vanderlinden LA, Zidek V, Silhavy J, Pravenec M, Hoffman PL, Tabakoff B. Unsupervised, Statistically Based Systems Biology Approach for Unraveling the Genetics of Complex Traits: A Demonstration with Ethanol Metabolism. Alcohol Clin Exp Res 2018; 42:1177-1191. [PMID: 29689131 DOI: 10.1111/acer.13763] [Citation(s) in RCA: 7] [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: 02/01/2018] [Accepted: 04/14/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND A statistical pipeline was developed and used for determining candidate genes and candidate gene coexpression networks involved in 2 alcohol (i.e., ethanol [EtOH]) metabolism phenotypes, namely alcohol clearance and acetate area under the curve in a recombinant inbred (RI) (HXB/BXH) rat panel. The approach was also used to provide an indication of how EtOH metabolism can impact the normal function of the identified networks. METHODS RNA was extracted from alcohol-naïve liver tissue of 30 strains of HXB/BXH RI rats. The reconstructed transcripts were quantitated, and data were used to construct gene coexpression modules and networks. A separate group of rats, comprising the same 30 strains, were injected with EtOH (2 g/kg) for measurement of blood EtOH and acetate levels. These data were used for quantitative trait loci (QTL) analysis of the rate of EtOH disappearance and circulating acetate levels. The analysis pipeline required calculation of the module eigengene values, the correction of these values with EtOH metabolism rates and acetate levels across the rat strains, and the determination of the eigengene QTLs. For a module to be considered a candidate for determining phenotype, the module eigengene values had to have significant correlation with the strain phenotypic values and the module eigengene QTLs had to overlap the phenotypic QTLs. RESULTS Of the 658 transcript coexpression modules generated from liver RNA sequencing data, a single module satisfied all criteria for being a candidate for determining the alcohol clearance trait. This module contained 2 alcohol dehydrogenase genes, including the gene whose product was previously shown to be responsible for the majority of alcohol elimination in the rat. This module was also the only module identified as a candidate for influencing circulating acetate levels. This module was also linked to the process of generation and utilization of retinoic acid as related to the autonomous immune response. CONCLUSIONS We propose that our analytical pipeline can successfully identify genetic regions and transcripts which predispose a particular phenotype and our analysis provides functional context for coexpression module components.
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Affiliation(s)
- Ryan Lusk
- Department of Pharmaceutical Sciences , Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado, Aurora, Colorado
| | - Laura M Saba
- Department of Pharmaceutical Sciences , Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado, Aurora, Colorado
| | - Lauren A Vanderlinden
- Department of Biostatistics and Informatics , Colorado School of Public Health, University of Colorado, Aurora, Colorado
| | - Vaclav Zidek
- Department of Model Diseases , Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Silhavy
- Department of Model Diseases , Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Pravenec
- Department of Model Diseases , Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Paula L Hoffman
- Department of Pharmaceutical Sciences , Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado, Aurora, Colorado.,Department of Pharmacology School of Medicine, University of Colorado, Aurora, Colorado
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences , Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado, Aurora, Colorado
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23
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Hoffman PL, Saba LM, Vanderlinden LA, Tabakoff B. Voluntary exposure to a toxin: the genetic influence on ethanol consumption. Mamm Genome 2017; 29:128-140. [PMID: 29196862 DOI: 10.1007/s00335-017-9726-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/22/2017] [Indexed: 02/07/2023]
Abstract
Ethyl alcohol is a toxin that, when consumed at high levels, produces organ damage and death. One way to prevent or ameliorate this damage in humans is to reduce the exposure of organs to alcohol by reducing alcohol ingestion. Both the propensity to consume large volumes of alcohol and the susceptibility of human organs to alcohol-induced damage exhibit a strong genetic influence. We have developed an integrative genetic/genomic approach to identify transcriptional networks that predispose complex traits, including propensity for alcohol consumption and propensity for alcohol-induced organ damage. In our approach, the phenotype is assessed in a panel of recombinant inbred (RI) rat strains, and quantitative trait locus (QTL) analysis is performed. Transcriptome data from tissues/organs of naïve RI rat strains are used to identify transcriptional networks using Weighted Gene Coexpression Network Analysis (WGCNA). Correlation of the first principal component of transcriptional coexpression modules with the phenotype across the rat strains, and overlap of QTLs for the phenotype and the QTLs for the coexpression modules (module eigengene QTL) provide the criteria for identification of the functionally related groups of genes that contribute to the phenotype (candidate modules). While we previously identified a brain transcriptional module whose QTL overlapped with a QTL for levels of alcohol consumption in HXB/BXH RI rat strains and 12 selected rat lines, this module did not account for all of the genetic variation in alcohol consumption. Our search for QTL overlap and correlation of coexpression modules with phenotype can, however, be applied to any organ in which the transcriptome has been measured, and this represents a holistic approach in the search for genetic contributors to complex traits. Previous work has implicated liver/brain interactions, particularly involving inflammatory/immune processes, as influencing alcohol consumption levels. We have now analyzed the liver transcriptome of the HXB/BXH RI rat panel in relation to the behavioral trait of alcohol consumption. We used RNA-Seq and microarray data to construct liver transcriptional networks, and identified a liver candidate transcriptional coexpression module that explained 24% of the genetic variance in voluntary alcohol consumption. The transcripts in this module focus attention on liver secretory products that influence inflammatory and immune signaling pathways. We propose that these liver secretory products can interact with brain mechanisms that affect alcohol consumption, and targeting these pathways provides a potential approach to reducing high levels of alcohol intake and also protecting the integrity of the liver and other organs.
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Affiliation(s)
- Paula L Hoffman
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado, Aurora, CO, 80045, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Laura M Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado, Aurora, CO, 80045, USA
| | - Lauren A Vanderlinden
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, 80045, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado, Aurora, CO, 80045, USA. .,Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd., Campus Box: C238, Aurora, CO, 80045, USA.
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24
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Duex JE, Owens C, Chauca-Diaz A, Dancik GM, Vanderlinden LA, Ghosh D, Leivo MZ, Hansel DE, Theodorescu D. Nuclear CD24 Drives Tumor Growth and Is Predictive of Poor Patient Prognosis. Cancer Res 2017; 77:4858-4867. [PMID: 28674079 PMCID: PMC5600841 DOI: 10.1158/0008-5472.can-17-0367] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/03/2017] [Accepted: 06/27/2017] [Indexed: 11/16/2022]
Abstract
Elevated tumor expression of the cell surface GPI-linked CD24 protein signals poor patient prognosis in many tumor types. However, some cancer cells selected to be negative for surface CD24 (surCD24-) still retain aggressive phenotypes in vitro and in vivo Here, we resolve this apparent paradox with the discovery of biologically active, nuclear CD24 (nucCD24) and finding that its levels are unchanged in surCD24- cells. Using the complementary techniques of biochemical cellular fractionation and immunofluorescence, we demonstrate a signal for CD24 in the nucleus in cells from various histologic types of cancer. Nuclear-specific expression of CD24 (NLS-CD24) increased anchorage-independent growth in vitro and tumor formation in vivo Immunohistochemistry of patient tumor samples revealed the presence of nucCD24, whose signal intensity correlated positively with the presence of metastatic disease. Analysis of gene expression between cells expressing CD24 and NLS-CD24 revealed a unique nucCD24 transcriptional signature. The median score derived from this signature was able to stratify overall survival in four patient datasets from bladder cancer and five patient datasets from colorectal cancer. Patients with high scores (more nucCD24-like) had reduced survival. These findings define a novel and functionally important intracellular location of CD24; they explain why surCD24- cells can remain aggressive, and they highlight the need to consider nucCD24 in both fundamental research and therapeutic development. Cancer Res; 77(18); 4858-67. ©2017 AACR.
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Affiliation(s)
- Jason E Duex
- Departments of Surgery and Pharmacology, University of Colorado, Aurora, Colorado
| | - Charles Owens
- Departments of Surgery and Pharmacology, University of Colorado, Aurora, Colorado
| | - Ana Chauca-Diaz
- Departments of Surgery and Pharmacology, University of Colorado, Aurora, Colorado
| | - Garrett M Dancik
- Department of Mathematics and Computer Science, Eastern Connecticut State University, Willimantic, Connecticut
| | - Lauren A Vanderlinden
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Colorado
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Colorado
| | - Mariah Z Leivo
- Department of Pathology, University of California San Diego, San Diego, California
| | - Donna E Hansel
- Department of Pathology, University of California San Diego, San Diego, California
| | - Dan Theodorescu
- Departments of Surgery and Pharmacology, University of Colorado, Aurora, Colorado.
- University of Colorado Comprehensive Cancer Center, Aurora, Colorado
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25
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Saba LM, Flink SC, Vanderlinden LA, Israel Y, Tampier L, Colombo G, Kiianmaa K, Bell RL, Printz MP, Flodman P, Koob G, Richardson HN, Lombardo J, Hoffman PL, Tabakoff B. The sequenced rat brain transcriptome--its use in identifying networks predisposing alcohol consumption. FEBS J 2015; 282:3556-78. [PMID: 26183165 DOI: 10.1111/febs.13358] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/10/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023]
Abstract
UNLABELLED A quantitative genetic approach, which involves correlation of transcriptional networks with the phenotype in a recombinant inbred (RI) population and in selectively bred lines of rats, and determination of coinciding quantitative trait loci for gene expression and the trait of interest, has been applied in the present study. In this analysis, a novel approach was used that combined DNA-Seq data, data from brain exon array analysis of HXB/BXH RI rat strains and six pairs of rat lines selectively bred for high and low alcohol preference, and RNA-Seq data (including rat brain transcriptome reconstruction) to quantify transcript expression levels, generate co-expression modules and identify biological functions that contribute to the predisposition of consuming varying amounts of alcohol. A gene co-expression module was identified in the RI rat strains that contained both annotated and unannotated transcripts expressed in the brain, and was associated with alcohol consumption in the RI panel. This module was found to be enriched with differentially expressed genes from the selected lines of rats. The candidate genes within the module and differentially expressed genes between high and low drinking selected lines were associated with glia (microglia and astrocytes) and could be categorized as being related to immune function, energy metabolism and calcium homeostasis, as well as glial-neuronal communication. The results of the present study show that there are multiple combinations of genetic factors that can produce the same phenotypic outcome. Although no single gene accounts for predisposition to a particular level of alcohol consumption in every animal model, coordinated differential expression of subsets of genes in the identified pathways produce similar phenotypic outcomes. DATABASE The datasets supporting the results of the present study are available at http://phenogen.ucdenver.edu.
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Affiliation(s)
- Laura M Saba
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA
| | - Stephen C Flink
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA
| | - Lauren A Vanderlinden
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA
| | - Yedy Israel
- Laboratory of Pharmacogenetics of Alcoholism, Molecular & Clinical Pharmacology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Lutske Tampier
- Laboratory of Pharmacogenetics of Alcoholism, Molecular & Clinical Pharmacology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Giancarlo Colombo
- Neuroscience Institute, National Research Council of Italy, Section of Cagliari, Monserrato, Italy
| | - Kalervo Kiianmaa
- Department of Alcohol, Drugs and Addiction, National Institute for Health and Welfare, Helsinki, Finland
| | - Richard L Bell
- Department of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Morton P Printz
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Pamela Flodman
- Department of Pediatrics, University of California, Irvine, Irvine, CA, USA
| | - George Koob
- Committee on the Neurobiology of Addiction Disorders, The Scripps Research Institute, La Jolla, CA, USA
| | - Heather N Richardson
- Committee on the Neurobiology of Addiction Disorders, The Scripps Research Institute, La Jolla, CA, USA
| | - Joseph Lombardo
- National Supercomputing Center for Energy and Environment, University of Nevada, Las Vegas, Nevada, USA
| | - Paula L Hoffman
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA.,Department of Pharmacology, University of Colorado Denver, Aurora, CO, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA.,Department of Pharmacology, University of Colorado Denver, Aurora, CO, USA
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26
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Zuo L, Lu L, Tan Y, Pan X, Cai Y, Wang X, Hong J, Zhong C, Wang F, Zhang XY, Vanderlinden LA, Tabakoff B, Luo X. Genome-wide association discoveries of alcohol dependence. Am J Addict 2015; 23:526-39. [PMID: 25278008 DOI: 10.1111/j.1521-0391.2014.12147.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 04/17/2014] [Accepted: 05/12/2014] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE To report the genome-wide significant and/or replicable risk variants for alcohol dependence and explore their potential biological functions. METHODS We searched in PubMed for all genome-wide association studies (GWASs) of alcohol dependence. The following three types of the results were extracted: genome-wide significant associations in an individual sample, the combined samples, or the meta-analysis (p < 5 × 10(-8) ); top-ranked associations in an individual sample (p < 10(-5) ) that were nominally replicated in other samples (p < .05); and nominally replicable associations across at least three independent GWAS samples (p < .05). These results were meta-analyzed. cis-eQTLs in human, RNA expression in rat and mouse brains and bioinformatics properties of all of these risk variants were analyzed. RESULTS The variants located within the alcohol dehydrogenase (ADH) cluster were significantly associated with alcohol dependence at the genome-wide level (p < 5 × 10(-8) ) in at least one sample. Some associations with the ADH cluster were replicable across six independent GWAS samples. The variants located within or near SERINC2, KIAA0040, MREG-PECR or PKNOX2 were significantly associated with alcohol dependence at the genome-wide level (p < 5 × 10(-8) ) in meta-analysis or combined samples, and these associations were replicable across at least one sample. The associations with the variants within NRD1, GPD1L-CMTM8 or MAP3K9-PCNX were suggestive (5 × 10(-8) < p < 10(-5) ) in some samples, and nominally replicable in other samples. The associations with the variants at HTR7 and OPA3 were nominally replicable across at least three independent GWAS samples (10(-5) < p < .05). Some risk variants at the ADH cluster, SERINC2, KIAA0040, NRD1, and HTR7 had potential biological functions. CONCLUSION The most robust risk locus was the ADH cluster. SERINC2, KIAA0040, NRD1, and HTR7 were also likely to play important roles in alcohol dependence. PKNOX2, MREG, PECR, GPD1L, CMTM8, MAP3K9, PCNX, and OPA3 might play less important roles in risk for alcohol dependence based on the function analysis. This conclusion will significantly contribute to the post-GWAS follow-up studies on alcohol dependence.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
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27
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Vanderlinden LA, Saba LM, Bennett B, Hoffman PL, Tabakoff B. Influence of sex on genetic regulation of "drinking in the dark" alcohol consumption. Mamm Genome 2015; 26:43-56. [PMID: 25559016 DOI: 10.1007/s00335-014-9553-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/17/2014] [Indexed: 10/24/2022]
Abstract
The ILSXISS (LXS) recombinant inbred (RI) panel of mice is a valuable resource for genetic mapping studies of complex traits, due to its genetic diversity and large number of strains. Male and female mice from this panel were used to investigate genetic influences on alcohol consumption in the "drinking in the dark" (DID) model. Male mice (38 strains) and female mice (36 strains) were given access to 20% ethanol during the early phase of their circadian dark cycle for four consecutive days. The first principal component of alcohol consumption measures on days 2, 3, and 4 was used as a phenotype (DID phenotype) to calculate QTLs, using a SNP marker set for the LXS RI panel. Five QTLs were identified, three of which included a significant genotype by sex interaction, i.e., a significant genotype effect in males and not females. To investigate candidate genes associated with the DID phenotype, data from brain microarray analysis (Affymetrix Mouse Exon 1.0 ST Arrays) of male LXS RI strains were combined with RNA-Seq data (mouse brain transcriptome reconstruction) from the parental ILS and ISS strains in order to identify expressed mouse brain transcripts. Candidate genes were determined based on common eQTL and DID phenotype QTL regions and correlation of transcript expression levels with the DID phenotype. The resulting candidate genes (in particular, Arntl/Bmal1) focused attention on the influence of circadian regulation on the variation in the DID phenotype in this population of mice.
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Affiliation(s)
- Lauren A Vanderlinden
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd., Campus Box: C238, Aurora, CO, 80045, USA,
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28
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Vanderlinden LA, Saba LM, Printz MP, Flodman P, Koob G, Richardson HN, Hoffman PL, Tabakoff B. Is the alcohol deprivation effect genetically mediated? Studies with HXB/BXH recombinant inbred rat strains. Alcohol Clin Exp Res 2014; 38:2148-57. [PMID: 24961585 DOI: 10.1111/acer.12471] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/16/2014] [Indexed: 01/23/2023]
Abstract
BACKGROUND Two features of alcohol addiction that have been widely studied in animal models are relapse drinking following periods of alcohol abstinence and the escalation of alcohol consumption after chronic continuous or intermittent alcohol exposure. The genetic contribution to these phenotypes has not been systematically investigated. METHODS HXB/BXH recombinant inbred (RI) rat strains were given access to alcohol sequentially as follows: alcohol (10%) as the only fluid for 1 week; alcohol (10%) and water in a 2-bottle choice paradigm for 7 weeks ("pre-alcohol deprivation effect [ADE] alcohol consumption"); 2 weeks of access to water only (alcohol deprivation); and 2 weeks of reaccess to 10% alcohol and water ("post-ADE alcohol consumption"). The periods of deprivation and reaccess to alcohol were repeated 3 times. The ADE was defined as the amount of alcohol consumed in the first 24 hours after deprivation minus the average daily amount of alcohol consumed in the week prior to deprivation. Heritability of the phenotypes was determined by analysis of variance, and quantitative trait loci (QTLs) were identified. RESULTS All strains showed increased alcohol consumption, compared to the predeprivation period, in the first 24 hours after each deprivation (ADE). Broad-sense heritability of the ADEs was low (ADE1, 9.1%; ADE2, 26.2%; ADE3, 16.3%). Alcohol consumption levels were relatively stable over weeks 2 to 7. Post-ADE alcohol consumption levels consistently increased in some strains and were decreased or unchanged in others. Heritability of pre- and post-ADE alcohol consumption was high and increased over time (week 2, 38.5%; week 7, 51.1%; week 11, 56.8%; week 15, 63.3%). QTLs for pre- and post-ADE alcohol consumption were similar, but the strength of the QTL association with the phenotype decreased over time. CONCLUSIONS In the HXB/BXH RI rat strains, genotypic variance does not account for a large proportion of phenotypic variance in the ADE phenotype (low heritability), suggesting a role of environmental factors. In contrast, a large proportion of the variance across the RI strains in pre- and post-ADE alcohol consumption is due to genetically determined variance (high heritability).
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Affiliation(s)
- Lauren A Vanderlinden
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado
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29
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O'Brien JH, Vanderlinden LA, Schedin PJ, Hansen KC. Rat mammary extracellular matrix composition and response to ibuprofen treatment during postpartum involution by differential GeLC-MS/MS analysis. J Proteome Res 2012; 11:4894-905. [PMID: 22897585 DOI: 10.1021/pr3003744] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Breast cancer patients diagnosed within five years following pregnancy have increased metastasis and decreased survival. A hallmark of postpartum biology that may contribute to this poor prognosis is mammary gland involution, involving massive epithelial cell death and dramatic stromal remodeling. Previous studies show pro-tumorigenic properties of extracellular matrix (ECM) isolated from rodent mammary glands undergoing postpartum involution. More recent work demonstrates systemic ibuprofen treatment during involution decreases its tumor-promotional nature. Utilizing a proteomics approach, we identified relative differences in the composition of mammary ECM isolated from nulliparous rats and those undergoing postpartum involution, with and without ibuprofen treatment. GeLC-MS/MS experiments resulted in 20327 peptide identifications that mapped to 884 proteins with a <0.02% false discovery rate. Label-free quantification yielded several ECM differences between nulliparous and involuting glands related to collagen-fiber organization, cell motility and attachment, and cytokine regulation. Increases in known pro-tumorigenic ECM proteins osteopontin, tenascin-C, and laminin-α1 and pro-inflammatory proteins STAT3 and CD68 further identify candidate mediators of breast cancer progression specific to the involution window. With postpartum ibuprofen treatment, decreases in tenascin-C and three laminin chains were revealed. Our data suggest novel ECM mediators of breast cancer progression and demonstrate a protective influence of ibuprofen on mammary ECM composition.
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Affiliation(s)
- Jenean H O'Brien
- School of Medicine, Division of Medical Oncology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, United States
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