1
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Bosenberg M, Liu ET, Yu CI, Palucka K. Mouse models for immuno-oncology. Trends Cancer 2023:S2405-8033(23)00041-9. [PMID: 37087398 DOI: 10.1016/j.trecan.2023.03.009] [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: 02/27/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 04/24/2023]
Abstract
Realizing the clinical promise of cancer immunotherapy is hindered by gaps in our knowledge of in vivo mechanisms underlying treatment response as well as treatment limiting toxicity. Preclinical in vivo model systems and technologies are required to address these knowledge gaps and to surmount the challenges faced in the clinical application of immunotherapy. Mice are commonly used for basic and translational research to support development and testing of immune interventions, including for cancer. Here, we discuss the advantages and the limitations of current models as well as future developments.
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Affiliation(s)
- Marcus Bosenberg
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA.
| | - Edison T Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA.
| | - Chun I Yu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA.
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2
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Aydin S, Pham DT, Zhang T, Keele GR, Skelly DA, Paulo JA, Pankratz M, Choi T, Gygi SP, Reinholdt LG, Baker CL, Churchill GA, Munger SC. Genetic dissection of the pluripotent proteome through multi-omics data integration. Cell Genom 2023; 3:100283. [PMID: 37082146 PMCID: PMC10112288 DOI: 10.1016/j.xgen.2023.100283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/12/2022] [Accepted: 02/27/2023] [Indexed: 04/22/2023]
Abstract
Genetic background drives phenotypic variability in pluripotent stem cells (PSCs). Most studies to date have used transcript abundance as the primary molecular readout of cell state in PSCs. We performed a comprehensive proteogenomics analysis of 190 genetically diverse mouse embryonic stem cell (mESC) lines. The quantitative proteome is highly variable across lines, and we identified pluripotency-associated pathways that were differentially activated in the proteomics data that were not evident in transcriptome data from the same lines. Integration of protein abundance to transcript levels and chromatin accessibility revealed broad co-variation across molecular layers as well as shared and unique drivers of quantitative variation in pluripotency-associated pathways. Quantitative trait locus (QTL) mapping localized the drivers of these multi-omic signatures to genomic hotspots. This study reveals post-transcriptional mechanisms and genetic interactions that underlie quantitative variability in the pluripotent proteome and provides a regulatory map for mESCs that can provide a basis for future mechanistic studies.
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Affiliation(s)
- Selcan Aydin
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Duy T. Pham
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Tian Zhang
- Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | - Ted Choi
- Predictive Biology, Inc., Carlsbad, CA 92010, USA
| | | | - Laura G. Reinholdt
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Christopher L. Baker
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Gary A. Churchill
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Steven C. Munger
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
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3
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Hedberg-Buenz A, Meyer KJ, van der Heide CJ, Deng W, Lee K, Soukup DA, Kettelson M, Pellack D, Mercer H, Wang K, Garvin MK, Abramoff MD, Anderson MG. Biological Correlations and Confounders for Quantification of Retinal Ganglion Cells by Optical Coherence Tomography Based on Studies of Outbred Mice. Transl Vis Sci Technol 2022; 11:17. [PMID: 36135979 PMCID: PMC9513741 DOI: 10.1167/tvst.11.9.17] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 08/02/2022] [Indexed: 01/28/2023] Open
Abstract
Purpose Despite popularity of optical coherence tomography (OCT) in glaucoma studies, it's unclear how well OCT-derived metrics compare to traditional measures of retinal ganglion cell (RGC) abundance. Here, Diversity Outbred (J:DO) mice are used to directly compare ganglion cell complex (GCC) thickness measured by OCT to metrics of retinal anatomy measured ex vivo with retinal wholemounts and optic nerve histology. Methods J:DO mice (n = 48) underwent fundoscopic and OCT examinations, with automated segmentation of GCC thickness. RGC axons were quantified from para-phenylenediamine-stained optic nerve cross-sections and somas from BRN3A-immunolabeled retinal wholemounts, with total inner retinal cellularity assessed by TO-PRO and subsequent hematoxylin staining. Results J:DO tissues lacked overt disease. GCC thickness, RGC abundance, and total cell abundance varied broadly across individuals. GCC thickness correlated significantly to RGC somal density (r = 0.58) and axon number (r = 0.44), but not total cell density. Retinal area and nerve cross-sectional area varied widely. No metrics were significantly influenced by sex. In bilateral comparisons, GCC thickness (r = 0.95), axon (r = 0.72), and total cell density (r = 0.47) correlated significantly within individuals. Conclusions Amongst outbred mice, OCT-derived measurements of GCC thickness correlate significantly to RGC somal and axon abundance. Factors limiting correlation are likely both biological and methodological, including differences in retinal area that distort sampling-based estimates of RGC abundance. Translational Relevance There are significant-but imperfect-correlations between GCC thickness and RGC abundance across genetic contexts in mice, highlighting valid uses and ongoing challenges for meaningful use of OCT-derived metrics.
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Affiliation(s)
- Adam Hedberg-Buenz
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Kacie J. Meyer
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Carly J. van der Heide
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Wenxiang Deng
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, USA
| | - Kyungmoo Lee
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, USA
| | - Dana A. Soukup
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Monica Kettelson
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA
| | - Danielle Pellack
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Hannah Mercer
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Kai Wang
- Department of Biostatistics, University of Iowa, Iowa City, IA, USA
| | - Mona K. Garvin
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, USA
| | - Michael D. Abramoff
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA
| | - Michael G. Anderson
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
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4
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Abstract
The diet and age of mice can modulate how different genetic variants impact body weight, demonstrating the need to take context into account when performing genetic studies.
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Affiliation(s)
- Hélène Tonnelé
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amelie Baud
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
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5
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Al-Shaer AE, Pal A, Shi Q, Carson MS, Regan J, Behee M, Buddenbaum N, Drawdy C, Davis T, Virk R, Shaikh SR. Modeling human heterogeneity of obesity with diversity outbred mice reveals a fat mass-dependent therapeutic window for resolvin E1. FASEB J 2022; 36:e22354. [PMID: 35616343 PMCID: PMC10027372 DOI: 10.1096/fj.202200350r] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 03/01/2022] [Revised: 04/27/2022] [Accepted: 05/06/2022] [Indexed: 11/11/2022]
Abstract
Resolvin E1 (RvE1), a specialized pro-resolving mediator (SPM), improves glucose homeostasis in inbred mouse models of obesity. However, an impediment toward translation is that obesity is a highly heterogenous disease in which individuals will respond very differently to interventions such as RvE1. Thus, there is a need to study SPMs in the context of modeling the heterogeneity of obesity that is observed in humans. We investigated how RvE1 controls the concentration of key circulating metabolic biomarkers using diversity outbred (DO) mice, which mimic human heterogeneity. We first demonstrate that weights of DO mice can be classified into distinct distributions of fat mass (i.e., modeling differing classes of obesity) in response to a high-fat diet and in the human population when examining body composition. Next, we show RvE1 administration based on body weight for four consecutive days after giving mice a high-fat diet led to approximately half of the mice responding positively for serum total gastric inhibitory polypeptide (GIP), glucagon, insulin, glucose, leptin, and resistin. Interestingly, RvE1 improved hyperleptinemia most effectively in the lowest class of fat mass despite adjusting the dose of RvE1 with increasing adiposity. Furthermore, leptin levels after RvE1 treatment were the lowest in those mice that were also RvE1 positive responders for insulin and resistin. Collectively, these results suggest a therapeutic fat mass-dependent window for RvE1, which should be considered in future clinical trials. Moreover, the data underscore the importance of studying SPMs with heterogenous mice as a step toward precision SPM administration in humans.
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Affiliation(s)
- Abrar E Al-Shaer
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anandita Pal
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Qing Shi
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Meredith S Carson
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer Regan
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Madeline Behee
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nicole Buddenbaum
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Catie Drawdy
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Traci Davis
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rafia Virk
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Saame Raza Shaikh
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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6
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Dobrinskikh E, Estrella AM, Hennessy CE, Hara N, Schwarz MI, Kurche JS, Yang IV, Schwartz DA. Genes, other than Muc5b, play a role in bleomycin-induced lung fibrosis. Am J Physiol Lung Cell Mol Physiol 2021; 321:L440-L450. [PMID: 34160296 PMCID: PMC8410112 DOI: 10.1152/ajplung.00615.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is an incurable genetic disease that affects 5 million people worldwide. The gain-of-function MUC5B promoter variant rs35705950 is the dominant genetic risk factor for IPF, yet has a low penetrance. This raises the possibility that other genes and transcripts affect the penetrance of MUC5B. Previously, we have shown that the concentration of Muc5b in bronchoalveolar epithelia is directly associated with the extent and persistence of bleomycin-induced lung fibrosis in mice. In this study, we investigated whether bleomycin-induced lung injury is Muc5b dependent in genetically divergent strains of mice. Specifically, mice from the eight Diversity Outbred (DO) founders were phenotyped for Muc5b expression and lung fibrosis 3 wk after intratracheal bleomycin administration. Although we identified strains with low Muc5b expression and minimal lung fibrosis (CAST/EiJ and PWK/PhJ) and strains with high Muc5b expression and extensive lung fibrosis (NZO/H1LtJ and WSB/EiJ), there also were strains that did not demonstrate a clear relationship between Muc5b expression and lung fibrosis (129S1/SvlmJ, NOD/ShiLtJ, and C57BL/6J, A/J). Hierarchical clustering suggests that other factors may work in concert with or potentially independent of Muc5b to promote bleomycin-induced lung injury and fibrosis. This study suggests that these strains and their recombinant inbred crosses may prove helpful in identifying the genes and transcripts that interact with Muc5b and cause lung fibrosis.
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Affiliation(s)
- Evgenia Dobrinskikh
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Alani M Estrella
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Corinne E Hennessy
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Naoko Hara
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Marvin I Schwarz
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Jonathan S Kurche
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Ivana V Yang
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - David A Schwartz
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado.,Department of Immunology, University of Colorado School of Medicine, Aurora, Colorado
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7
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Pal A, Al-Shaer AE, Guesdon W, Torres MJ, Armstrong M, Quinn K, Davis T, Reisdorph N, Neufer PD, Spangenburg EE, Carroll I, Bazinet RP, Halade GV, Clària J, Shaikh SR. Resolvin E1 derived from eicosapentaenoic acid prevents hyperinsulinemia and hyperglycemia in a host genetic manner. FASEB J 2020; 34:10640-10656. [PMID: 32579292 PMCID: PMC7497168 DOI: 10.1096/fj.202000830r] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 04/07/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022]
Abstract
Eicosapentaenoic acid (EPA) has garnered attention after the success of the REDUCE‐IT trial, which contradicted previous conclusions on EPA for cardiovascular disease risk. Here we first investigated EPA's preventative role on hyperglycemia and hyperinsulinemia. EPA ethyl esters prevented obesity‐induced glucose intolerance, hyperinsulinemia, and hyperglycemia in C57BL/6J mice. Supporting NHANES analyses showed that fasting glucose levels of obese adults were inversely related to EPA intake. We next investigated how EPA improved murine hyperinsulinemia and hyperglycemia. EPA overturned the obesity‐driven decrement in the concentration of 18‐hydroxyeicosapentaenoic acid (18‐HEPE) in white adipose tissue and liver. Treatment of obese inbred mice with RvE1, the downstream immunoresolvant metabolite of 18‐HEPE, but not 18‐HEPE itself, reversed hyperinsulinemia and hyperglycemia through the G‐protein coupled receptor ERV1/ChemR23. To translate the findings, we determined if the effects of RvE1 were dependent on host genetics. RvE1's effects on hyperinsulinemia and hyperglycemia were divergent in diversity outbred mice that model human genetic variation. Secondary SNP analyses further confirmed extensive genetic variation in human RvE1/EPA‐metabolizing genes. Collectively, the data suggest EPA prevents hyperinsulinemia and hyperglycemia, in part, through RvE1's activation of ERV1/ChemR23 in a host genetic manner. The studies underscore the need for personalized administration of RvE1 based on genetic/metabolic enzyme profiles.
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Affiliation(s)
- Anandita Pal
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Abrar E Al-Shaer
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William Guesdon
- Department of Biochemistry & Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Maria J Torres
- Department of Physiology, East Carolina Diabetes & Obesity Institute, East Carolina University, Greenville, NC, USA
| | - Michael Armstrong
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Kevin Quinn
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Traci Davis
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nichole Reisdorph
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - P Darrell Neufer
- Department of Physiology, East Carolina Diabetes & Obesity Institute, East Carolina University, Greenville, NC, USA
| | - Espen E Spangenburg
- Department of Physiology, East Carolina Diabetes & Obesity Institute, East Carolina University, Greenville, NC, USA
| | - Ian Carroll
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard P Bazinet
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Ganesh V Halade
- Division of Cardiovascular Sciences, Department of Medicine, The University of South Florida, Tampa, FL, USA
| | - Joan Clària
- Department of Biochemistry and Molecular Genetics, University of Barcelona, Hospital Clínic, Barcelona, Spain
| | - Saame Raza Shaikh
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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8
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Recla JM, Bubier JA, Gatti DM, Ryan JL, Long KH, Robledo RF, Glidden NC, Hou G, Churchill GA, Maser RS, Zhang ZW, Young EE, Chesler EJ, Bult CJ. Genetic mapping in Diversity Outbred mice identifies a Trpa1 variant influencing late-phase formalin response. Pain 2019; 160:1740-1753. [PMID: 31335644 PMCID: PMC6668363 DOI: 10.1097/j.pain.0000000000001571] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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] [Indexed: 12/20/2022]
Abstract
Identification of genetic variants that influence susceptibility to pain is key to identifying molecular mechanisms and targets for effective and safe therapeutic alternatives to opioids. To identify genes and variants associated with persistent pain, we measured late-phase response to formalin injection in 275 male and female Diversity Outbred mice genotyped for over 70,000 single nucleotide polymorphisms. One quantitative trait locus reached genome-wide significance on chromosome 1 with a support interval of 3.1 Mb. This locus, Nociq4 (nociceptive sensitivity quantitative trait locus 4; MGI: 5661503), harbors the well-known pain gene Trpa1 (transient receptor potential cation channel, subfamily A, member 1). Trpa1 is a cation channel known to play an important role in acute and chronic pain in both humans and mice. Analysis of Diversity Outbred founder strain allele effects revealed a significant effect of the CAST/EiJ allele at Trpa1, with CAST/EiJ carrier mice showing an early, but not late, response to formalin relative to carriers of the 7 other inbred founder alleles (A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ). We characterized possible functional consequences of sequence variants in Trpa1 by assessing channel conductance, TRPA1-TRPV1 interactions, and isoform expression. The phenotypic differences observed in CAST/EiJ relative to C57BL/6J carriers were best explained by Trpa1 isoform expression differences, implicating a splice junction variant as the causal functional variant. This study demonstrates the utility of advanced, high-precision genetic mapping populations in resolving specific molecular mechanisms of variation in pain sensitivity.
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Affiliation(s)
- Jill M. Recla
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- IGERT Program in Functional Genomics, Graduate School of Biomedical Sciences and Engineering, The University of Maine, Orono, ME 04469, USA
| | - Jason A. Bubier
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Daniel M. Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jennifer L. Ryan
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Katie H. Long
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Nicole C. Glidden
- Department of Genetics and Genome Sciences, UCONN Health, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Guoqiang Hou
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Richard S. Maser
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Zhong-wei Zhang
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Erin E. Young
- Department of Genetics and Genome Sciences, UCONN Health, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
- School of Nursing, University of Connecticut, 231 Glenbrook Rd, Unit 4026, Storrs, CT 06269-4026, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269-4026, USA
| | | | - Carol J. Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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9
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Coffey AR, Smallwood TL, Albright J, Hua K, Kanke M, Pomp D, Bennett BJ, Sethupathy P. Systems genetics identifies a co-regulated module of liver microRNAs associated with plasma LDL cholesterol in murine diet-induced dyslipidemia. Physiol Genomics 2017; 49:618-629. [PMID: 28916633 DOI: 10.1152/physiolgenomics.00050.2017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/21/2017] [Accepted: 09/12/2017] [Indexed: 02/06/2023] Open
Abstract
Chronically altered levels of circulating lipids, termed dyslipidemia, is a significant risk factor for a number of metabolic and cardiovascular morbidities. MicroRNAs (miRNAs) have emerged as important regulators of lipid balance, have been implicated in dyslipidemia, and have been proposed as candidate therapeutic targets in lipid-related disorders including atherosclerosis. A major limitation of most murine studies of miRNAs in lipid metabolic disorders is that they have been performed in just one (or very few) inbred strains, such as C57BL/6. Moreover, although individual miRNAs have been associated with lipid phenotypes, it is well understood that miRNAs likely work together in functional modules. To address these limitations, we implemented a systems genetics strategy using the Diversity Outbred (DO) mouse population. Specifically, we performed gene and miRNA expression profiling in the livers from ~300 genetically distinct DO mice after 18 wk on either a high-fat/high-cholesterol diet or a high-protein diet. Large-scale correlative analysis of these data with a wide range of cardio-metabolic end points revealed a co-regulated module of miRNAs significantly associated with circulating low-density lipoprotein cholesterol (LDL-C) levels. The hubs of this module were identified as miR-199a, miR-181b, miR-27a, miR-21_-_1, and miR-24. In sum, we demonstrate that a high-fat/high-cholesterol diet robustly rewires the miRNA regulatory network, and we identify a small group of co-regulated miRNAs that may exert coordinated effects to control circulating LDL-C.
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Affiliation(s)
- Alisha R Coffey
- Curriculum in Genetics and Molecular Biology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | - Tangi L Smallwood
- Department of Genetics, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | - Jody Albright
- US Department of Agriculture, ARS Western Human Nutrition Research Center, University of California, Davis, Davis, California; and
| | - Kunjie Hua
- Department of Genetics, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Daniel Pomp
- Department of Genetics, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | - Brian J Bennett
- Curriculum in Genetics and Molecular Biology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, North Carolina.,US Department of Agriculture, ARS Western Human Nutrition Research Center, University of California, Davis, Davis, California; and
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
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