1
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Johnson LL, Abrahante JE, McLoon LK. Nystagmus in the B6(CG)Tyr(c-2J)/J Albino Mouse: A Functional and RNA-Seq Analysis. Invest Ophthalmol Vis Sci 2024; 65:26. [PMID: 38206276 PMCID: PMC10787582 DOI: 10.1167/iovs.65.1.26] [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: 07/24/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Purpose Infantile nystagmus syndrome (INS) is a gaze-holding disorder characterized by conjugate, uncontrolled eye oscillations that can result in significant visual acuity loss. INS is often associated with albinism, but the mechanism is unclear. Albino mice have nystagmus; however, a pigmented mouse with a tyr mutation making it phenotypically albino, the B6(CG)-Tyr(c-2J)/J (B6 albino), had not been tested. We tested optokinetic response (OKR) in B6 albino and control mice. RNA-Seq was performed on extraocular muscles (EOM), tibialis anterior (TA) muscle, abducens (CN6), and oculomotor (CN3) neurons to uncover molecular differences that may contribute to nystagmus. Methods OKR was measured using an ISCAN system. RNA was isolated from four tissues to identify differentially expressed genes and validated with qPCR and immunohistochemistry. Ingenuity pathway analyses identified top biological pathways. Results All B6 albino mice tested had nystagmus. Differential RNA expression analysis showed 383 genes differentially expressed in EOM, 70 in CN3, 20 in CN6, and 639 in the TA. Two genes were differentially expressed in all four tissues: wdfy1 and nnt. Differences were validated by qPCR and immunostaining. Conclusions The tyr mutation in B6 albino mice, genotypically pigmented and phenotypically albino, is sufficient to result in spontaneous nystagmus. The two genes with decreased expression in the B6 albino tissues examined, wdfy1 and nnt, have been implicated in mitochondrial dysfunction and stem cell maintenance in other systems. Their function in extraocular muscle is unknown. These studies suggest that this mouse model of nystagmus may allow molecular identification of candidate nystagmus-related genes.
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Affiliation(s)
- Laura L. Johnson
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, United States
- Graduate Program in Cellular, Molecular, Developmental Biology and Genetics, University of Minnesota, Minneapolis, Minnesota, United States
| | - Juan E. Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, Minnesota, United States
| | - Linda K. McLoon
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, United States
- Graduate Program in Cellular, Molecular, Developmental Biology and Genetics, University of Minnesota, Minneapolis, Minnesota, United States
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2
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BoYe, Bradshaw AD, Abrahante JE, Dragon JA, Häußler TN, Bell SP, Hirashima F, LeWinter M, Zile MR, Meyer M. Left Ventricular Gene Expression in Heart Failure With Preserved Ejection Fraction-Profibrotic and Proinflammatory Pathways and Genes. Circ Heart Fail 2023; 16:e010395. [PMID: 37582166 PMCID: PMC10430768 DOI: 10.1161/circheartfailure.123.010395] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/16/2023] [Indexed: 08/17/2023]
Abstract
BACKGROUND Heart failure with preserved ejection fraction (HFpEF) is increasingly prevalent and has few treatments. The molecular mechanisms and resultant signaling pathways that underlie the development of HFpEF are poorly defined. It has been proposed that activation of proinflammatory pathways plays a role in the development of cardiac fibrosis. The signature of gene expression (transcriptome) of previously validated left ventricular biopsies obtained from patients with HFpEF and matched referent controls allows for an unbiased assessment of proinflammatory and profibrotic signaling pathways and genes. METHODS Epicardial left ventricular biopsies from stringently selected HFpEF patients (HFpEF, n=16) and referent control patients (CTR, n=14) were obtained during aortocoronary bypass surgery. The subepicardial myocardium was flash-frozen to build a repository that was parallel-processed for RNA sequencing to allow for an unsupervised in-depth comparison of the left ventricular transcriptome. RESULTS The average patient age was 67±10 years. When compared with controls, patients with HFpEF were hypertensive with a higher body mass index (kg/m2: 30±5 versus 37±6; P<0.01) and elevated NT-proBNP levels (pg/mL: 155 [89-328] versus 1554 [888-2178]; P<0.001). The transcriptome analysis revealed differential expression of 477 genes many of which were involved in profibrotic pathways including extracellular matrix production and posttranslational modification but no proinflammatory signature. CONCLUSIONS The transcriptome analysis of left ventricular myocardial samples from patients with HFpEF confirms an overabundant extracellular matrix gene expression, the basis of myocardial fibrosis, without a signature of activated proinflammatory pathways or genes.
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Affiliation(s)
- BoYe
- Lillehei Heart Institute and Genomics Center of the University of Minnesota, Minneapolis, MN, USA
| | - Amy D Bradshaw
- Medical University of South Carolina, RHJ Department of Veterans Affairs Medical Center, Charleston, SC, USA
| | - Juan E. Abrahante
- Lillehei Heart Institute and Genomics Center of the University of Minnesota, Minneapolis, MN, USA
| | - Julie A. Dragon
- University of Vermont Medical Center, Cardiology, Cardiothoracic Surgery and Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Tim N. Häußler
- University of Vermont Medical Center, Cardiology, Cardiothoracic Surgery and Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Stephen P. Bell
- University of Vermont Medical Center, Cardiology, Cardiothoracic Surgery and Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Fuyuki Hirashima
- University of Vermont Medical Center, Cardiology, Cardiothoracic Surgery and Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Martin LeWinter
- University of Vermont Medical Center, Cardiology, Cardiothoracic Surgery and Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Michael R. Zile
- Medical University of South Carolina, RHJ Department of Veterans Affairs Medical Center, Charleston, SC, USA
| | - Markus Meyer
- Lillehei Heart Institute and Genomics Center of the University of Minnesota, Minneapolis, MN, USA
- University of Vermont Medical Center, Cardiology, Cardiothoracic Surgery and Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
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3
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Garay BI, Givens S, Abreu P, Liu M, Yücel D, Baik J, Stanis N, Rothermel TM, Magli A, Abrahante JE, Goloviznina NA, Soliman HA, Dhoke NR, Kyba M, Alford PW, Dudley SC, van Berlo JH, Ogle B, Perlingeiro RR. Dual inhibition of MAPK and PI3K/AKT pathways enhances maturation of human iPSC-derived cardiomyocytes. Stem Cell Reports 2023; 18:411. [PMID: 36630905 PMCID: PMC9860141 DOI: 10.1016/j.stemcr.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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4
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Miller S, Abrahante JE, Roopra A, Dougherty BJ. A transcriptome dataset for gonadectomy-induced changes in rat spinal cord. Sci Data 2022; 9:789. [PMID: 36581616 PMCID: PMC9800375 DOI: 10.1038/s41597-022-01917-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022] Open
Abstract
Circulating sex steroid hormones are critical for neural function and development of neuroplasticity in many regions of the central nervous system. In the spinal cord, our knowledge of steroid hormone influence mostly derives from mechanistic studies of pain processing in dorsal spinal cord circuits; less is known regarding hormonal influence of ventral spinal motor function. Gonadectomy (surgical removal of the testes in males and ovaries in females) rapidly and persistently reduces circulating sex steroids in both females and males, providing a means to interrogate the role of hormones on neural function. Here we provide a next-generation RNA sequencing (RNA-seq) data set to evaluate the impact of gonadectomy on the transcriptome of ventral spinal cord tissue of adult female and male rats.
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Affiliation(s)
- Shawn Miller
- Divisions of Physical Therapy and Rehabilitation Science, Department of Rehabilitation Medicine, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN, 55455, USA
| | - Avtar Roopra
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53705, USA
| | - Brendan J Dougherty
- Divisions of Physical Therapy and Rehabilitation Science, Department of Rehabilitation Medicine, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
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5
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Garay BI, Givens S, Abreu P, Liu M, Yücel D, Baik J, Stanis N, Rothermel TM, Magli A, Abrahante JE, Goloviznina NA, Soliman HAN, Dhoke NR, Kyba M, Alford PW, Dudley SC, van Berlo JH, Ogle B, Perlingeiro RRC. Dual inhibition of MAPK and PI3K/AKT pathways enhances maturation of human iPSC-derived cardiomyocytes. Stem Cell Reports 2022; 17:2005-2022. [PMID: 35931076 PMCID: PMC9481895 DOI: 10.1016/j.stemcr.2022.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 11/12/2021] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 01/25/2023] Open
Abstract
Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide great opportunities for mechanistic dissection of human cardiac pathophysiology; however, hiPSC-CMs remain immature relative to the adult heart. To identify novel signaling pathways driving the maturation process during heart development, we analyzed published transcriptional and epigenetic datasets from hiPSC-CMs and prenatal and postnatal human hearts. These analyses revealed that several components of the MAPK and PI3K-AKT pathways are downregulated in the postnatal heart. Here, we show that dual inhibition of these pathways for only 5 days significantly enhances the maturation of day 30 hiPSC-CMs in many domains: hypertrophy, multinucleation, metabolism, T-tubule density, calcium handling, and electrophysiology, many equivalent to day 60 hiPSC-CMs. These data indicate that the MAPK/PI3K/AKT pathways are involved in cardiomyocyte maturation and provide proof of concept for the manipulation of key signaling pathways for optimal hiPSC-CM maturation, a critical aspect of faithful in vitro modeling of cardiac pathologies and subsequent drug discovery.
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Affiliation(s)
- Bayardo I Garay
- Lillehei Heart Institute (LHI), Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA; Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Sophie Givens
- Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Phablo Abreu
- Lillehei Heart Institute (LHI), Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Man Liu
- Lillehei Heart Institute (LHI), Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Doğacan Yücel
- Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - June Baik
- Lillehei Heart Institute (LHI), Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Noah Stanis
- Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
| | | | - Alessandro Magli
- Lillehei Heart Institute (LHI), Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN, USA
| | - Natalya A Goloviznina
- Molecular, Cellular, Developmental Biology and Genetics, University of Minnesota, Minneapolis, MN, USA; LHI, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Hossam A N Soliman
- LHI, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Neha R Dhoke
- Lillehei Heart Institute (LHI), Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Michael Kyba
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA; Molecular, Cellular, Developmental Biology and Genetics, University of Minnesota, Minneapolis, MN, USA; LHI, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Patrick W Alford
- Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Samuel C Dudley
- Lillehei Heart Institute (LHI), Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Jop H van Berlo
- Lillehei Heart Institute (LHI), Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA; Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Brenda Ogle
- Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Rita R C Perlingeiro
- Lillehei Heart Institute (LHI), Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA; Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA; Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA; Molecular, Cellular, Developmental Biology and Genetics, University of Minnesota, Minneapolis, MN, USA.
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6
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Shang L, Aughey E, Kim H, Heden TD, Wang L, Najt CP, Esch N, Brunko S, Abrahante JE, Macchietto M, Mashek MT, Fairbanks T, Promislow DEL, Neufeld TP, Mashek DG. Systemic lipolysis promotes physiological fitness in Drosophila melanogaster. Aging (Albany NY) 2022; 14:6481-6506. [PMID: 36044277 PMCID: PMC9467406 DOI: 10.18632/aging.204251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 03/04/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022]
Abstract
Since interventions such as caloric restriction or fasting robustly promote lipid catabolism and improve aging-related phenotypical markers, we investigated the direct effect of increased lipid catabolism via overexpression of bmm (brummer, FBgn0036449), the major triglyceride hydrolase in Drosophila, on lifespan and physiological fitness. Comprehensive characterization was carried out using RNA-seq, lipidomics and metabolomics analysis. Global overexpression of bmm strongly promoted numerous markers of physiological fitness, including increased female fecundity, fertility maintenance, preserved locomotion activity, increased mitochondrial biogenesis and oxidative metabolism. Increased bmm robustly upregulated the heat shock protein 70 (Hsp70) family of proteins, which equipped the flies with higher resistance to heat, cold, and ER stress via improved proteostasis. Despite improved physiological fitness, bmm overexpression did not extend lifespan. Taken together, these data show that bmm overexpression has broad beneficial effects on physiological fitness, but these effects did not impact lifespan.
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Affiliation(s)
- Linshan Shang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Elizabeth Aughey
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Huiseon Kim
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy D Heden
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105, USA
| | - Charles P Najt
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nicholas Esch
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sophia Brunko
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN 55455, USA
| | - Marissa Macchietto
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mara T Mashek
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Todd Fairbanks
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel E L Promislow
- Department of Biology, University of Washington, Seattle, WA 98195, USA.,Department of Lab Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Thomas P Neufeld
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Douglas G Mashek
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, University of Minnesota, Minneapolis, MN 55455, USA
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7
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Sosa F, Santos JEP, Rae DO, Larson CC, Macchietto M, Abrahante JE, Amaral TF, Denicol AC, Sonstegard TS, Hansen PJ. Effects of the SLICK1 mutation in PRLR on regulation of core body temperature and global gene expression in liver in cattle. Animal 2022; 16:100523. [PMID: 35468510 DOI: 10.1016/j.animal.2022.100523] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 11/01/2022] Open
Abstract
The SLICK1 mutation in bovine PRLR (c.1382del; rs517047387) is a deletion mutation resulting in a protein with a truncated intracellular domain. Cattle carrying at least one allele have a phenotype characterized by a short hair coat (slick phenotype) and increased resistance to heat stress. Given the pleiotropic nature of prolactin, the mutation may affect other physiological characteristics. The liver is one organ that could potentially be affected because of the expression of PRLR. The mutation is a dominant allele, and heterozygous animals have a similar hair coat to that of animals homozygous for the mutation. Present objectives were to determine whether inheritance of the SLICK1 mutation affects liver gene expression and if animals homozygous for the SLICK1 allele differ from heterozygotes in liver gene expression and regulation of body temperature during heat stress. In one experiment, rectal and ruminal temperatures were less for Holstein heifers that were heterozygous for the SLICK1 allele compared with wildtype heifers. There were 71 differentially expressed genes in liver, with 13 upregulated and 58 downregulated in SLICK1 heterozygotes. Among the ontologies characteristic of differentially expressed genes were those related to immune function and fatty acid and amino acid metabolism. In a prospective cohort study conducted with adult Senepol cattle, body temperature and hepatic gene expression were compared between animals heterozygous or homozygous for the SLICK1 mutation. There were no differences in ruminal temperatures between genotypes, rectal temperature was higher in animals homozygous for the SLICK1 mutation, and there was only one gene in liver that was differentially expressed. It was concluded that inheritance of the SLICK1 allele can exert functional changes beyond those related to hair growth although changes in liver gene expression were not extensive. Results are also consistent with the SLICK1 allele being dominant because there were few differences in phenotype between animals inheriting one or two copies of the allele.
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Affiliation(s)
- Froylan Sosa
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
| | - José E P Santos
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
| | - D Owen Rae
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville 32610-0136, USA
| | - Colleen C Larson
- Okeechobee County Cooperative Extension Service, University of Florida/Institute of Food and Agricultural Sciences, Okeechobee, FL 34972, USA
| | - Marissa Macchietto
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Juan E Abrahante
- Informatics Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Thiago F Amaral
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
| | - Anna C Denicol
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | | | - Peter J Hansen
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA.
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8
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Sariol A, Zhao J, Abrahante JE, Perlman S. Virus-Specific Regulatory T Cells Persist as Memory in a Neurotropic Coronavirus Infection. J I 2022; 208:1989-1997. [PMID: 35365567 PMCID: PMC9012697 DOI: 10.4049/jimmunol.2100794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/04/2022] [Indexed: 11/19/2022]
Abstract
Regulatory T cells (Tregs) are critical for regulating immunopathogenic responses in a variety of infections, including infection of mice with JHM strain of mouse hepatitis virus (JHMV), a neurotropic coronavirus that causes immune-mediated demyelinating disease. Although virus-specific Tregs are known to mitigate disease in this infection by suppressing pathogenic effector T cell responses of the same specificity, it is unclear whether these virus-specific Tregs form memory populations and persist similar to their conventional T cell counterparts of the same epitope specificity. Using congenically labeled JHMV-specific Tregs, we found that virus-specific Tregs persist long-term after murine infection, through at least 180 d postinfection and stably maintain Foxp3 expression. We additionally demonstrate that these cells are better able to proliferate and inhibit virus-specific T cell responses postinfection than naive Tregs of the same specificity, further suggesting that these cells differentiate into memory Tregs upon encountering cognate Ag. Taken together, these data suggest that virus-specific Tregs are able to persist long-term in the absence of viral Ag as memory Tregs.
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Affiliation(s)
- Alan Sariol
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; and
| | | | - Stanley Perlman
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA;
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA
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9
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Braunlin E, Abrahante JE, McElmurry R, Evans M, Smith M, Seelig D, O'Sullivan MG, Tolar J, Whitley CB, McIvor RS. Contribution of the innate and adaptive immune systems to aortic dilation in murine mucopolysaccharidosis type I. Mol Genet Metab 2022; 135:193-205. [PMID: 35165009 PMCID: PMC9109621 DOI: 10.1016/j.ymgme.2022.01.104] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/23/2021] [Accepted: 01/31/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND Adult immunocompetent male C57Bl/6 mucopolysaccharidosis, type I (MPSI) mice develop aortic insufficiency (AI), dilated ascending aortas and decreased cardiac function, findings not observed in immune incompetent adult male NSG MPSI mice. We sought to determine why. METHODS Cardiac ultrasound measurements of ascending aorta and left ventricular dimensions and Doppler interrogation for AI were performed in 6-month-old male B6 MPSI (N = 12), WT (N = 6), NSG MPSI (N = 8), NSG (N = 6) mice. Urinary glycosaminoglycans, RNA sequencing with quantitative PCR were performed and aortic pathology assessed by routine and immunohistochemical staining on subsets of murine aortas. RESULTS Ascending aortic diameters were significantly greater, left ventricular function significantly decreased, and AI significantly more frequent in B6 MPSI mice compared to NSG MPSI mice (p < 0.0001, p = 0.008 and p = 0.02, respectively); NSG and B6 WT mice showed no changes. Urinary glycosaminoglycans were significantly greater in B6 and NSG MPSI mice and both were significantly elevated compared to WT controls (p = 0.003 and p < 0.0001, respectively). By RNA sequencing, all 11 components of the inflammasome pathway were upregulated in B6 MUT, but only Aim2 and Ctsb in NSG MUT mice and none in WT controls. Both B6 and NSG MUT mice demonstrated variably-severe intramural inflammation, vacuolated cells, elastin fragmentation and disarray, and intense glycosaminoglycans on histological staining. B6 MPSI mice demonstrated numerous medial MAC2+ macrophages and adventitial CD3+ T-cells while MAC2+ macrophages were sparse and CD3+ T-cells absent in NSG MPSI mice. CONCLUSIONS Aortic dilation, AI and decreased cardiac function occur in immunocompetent B6 MPSI male mice but not in immune incompetent NSG MPSI mice, unrelated to GAG excretion, upregulation of Ctsb, or routine histologic appearance. Upregulation of all components of the inflammasome pathway in B6 MUT, but not NSG MUT mice, and abundant medial MAC2 and adventitial CD3 infiltrates in B6, but not NSG, MPSI aortas differentiated the two strains. These results suggest that the innate and adaptive immune systems play a role in these cardiac findings which may be relevant to human MPSI.
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Affiliation(s)
- Elizabeth Braunlin
- Department of Pediatrics University of Minnesota Medical School, Minneapolis, MN, USA.
| | - Juan E Abrahante
- University of Minnesota Informatics Institute University of Minnesota, Minneapolis, MN, USA.
| | - Ron McElmurry
- Department of Pediatrics University of Minnesota Medical School, Minneapolis, MN, USA.
| | - Michael Evans
- Biostatistical Design and Analysis Center Clinical and Translational Science Institute University of Minnesota Medical School, Minneapolis, MN, USA.
| | - Miles Smith
- Department of Genetics, Cell Biology and Development University of Minnesota Medical School, Minneapolis, MN, USA.
| | - Davis Seelig
- Comparative Pathology Shared Resource, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, St. Paul, MN, USA.
| | - M Gerard O'Sullivan
- Comparative Pathology Shared Resource, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, St. Paul, MN, USA.
| | - Jakub Tolar
- Department of Blood and Marrow Transplant University of Minnesota Medical School, Minneapolis, MN, USA.
| | - Chester B Whitley
- Gene Therapy Center Department of Pediatrics University of Minnesota Medical School Minneapolis, MN, USA.
| | - R Scott McIvor
- Department of Genetics, Cell Biology and Development University of Minnesota Medical School, Minneapolis, MN, USA.
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10
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McCartney MA, Auch B, Kono T, Mallez S, Zhang Y, Obille A, Becker A, Abrahante JE, Garbe J, Badalamenti JP, Herman A, Mangelson H, Liachko I, Sullivan S, Sone ED, Koren S, Silverstein KAT, Beckman KB, Gohl DM. The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol. G3 (Bethesda) 2022; 12:6460334. [PMID: 34897429 PMCID: PMC9210306 DOI: 10.1093/g3journal/jkab423] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023]
Abstract
The zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for Dreissena or related bivalves. Although the D. polymorpha genome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate a high-quality chromosome-scale genome assembly. Through comparative analysis and transcriptomics experiments, we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact steamer-like elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found that D. polymorpha have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.
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Affiliation(s)
- Michael A McCartney
- Department of Fisheries, Wildlife and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, St. Paul, MN 55108, USA
| | - Benjamin Auch
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Thomas Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sophie Mallez
- Department of Fisheries, Wildlife and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, St. Paul, MN 55108, USA
| | - Ying Zhang
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Angelico Obille
- Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Aaron Becker
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN 55455, USA
| | - John Garbe
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | | | - Adam Herman
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | - Eli D Sone
- Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.,Department of Materials Science & Engineering, University of Toronto, Toronto, ON M5S 3E4 Canada.,Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Kevin A T Silverstein
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA.,Department of Genetics, Cell Biology, and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA
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11
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Colonnetta MM, Abrahante JE, Schedl P, Gohl DM, Deshpande G. CLAMP regulates zygotic genome activation in Drosophila embryos. Genetics 2021; 219:iyab107. [PMID: 34849887 PMCID: PMC8633140 DOI: 10.1093/genetics/iyab107] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/15/2020] [Indexed: 11/13/2022] Open
Abstract
Embryonic patterning is critically dependent on zygotic genome activation (ZGA). In Drosophila melanogaster embryos, the pioneer factor Zelda directs ZGA, possibly in conjunction with other factors. Here, we have explored the novel involvement of Chromatin-Linked Adapter for MSL Proteins (CLAMP) during ZGA. CLAMP binds thousands of sites genome-wide throughout early embryogenesis. Interestingly, CLAMP relocates to target promoter sequences across the genome when ZGA is initiated. Although there is a considerable overlap between CLAMP and Zelda binding sites, the proteins display distinct temporal dynamics. To assess whether CLAMP occupancy affects gene expression, we analyzed transcriptomes of embryos zygotically compromised for either clamp or zelda and found that transcript levels of many zygotically activated genes are similarly affected. Importantly, compromising either clamp or zelda disrupted the expression of critical segmentation and sex determination genes bound by CLAMP (and Zelda). Furthermore, clamp knockdown embryos recapitulate other phenotypes observed in Zelda-depleted embryos, including nuclear division defects, centrosome aberrations, and a disorganized actomyosin network. Based on these data, we propose that CLAMP acts in concert with Zelda to regulate early zygotic transcription.
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Affiliation(s)
- Megan M Colonnetta
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN 55455, USA
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Girish Deshpande
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
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12
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Reed KM, Mendoza KM, Abrahante JE, Velleman SG, Strasburg GM. Data Mining Identifies Differentially Expressed Circular RNAs in Skeletal Muscle of Thermally Challenged Turkey Poults. Front Physiol 2021; 12:732208. [PMID: 34512399 PMCID: PMC8424120 DOI: 10.3389/fphys.2021.732208] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/06/2021] [Indexed: 11/30/2022] Open
Abstract
Precise regulation of gene expression is critical for normal muscle growth and development. Changes in gene expression patterns caused by external stressors such as temperature can have dramatic effects including altered cellular structure and function. Understanding the cellular mechanisms that underlie muscle growth and development and how these are altered by external stressors are crucial in maintaining and improving meat quality. This study investigated circular RNAs (circRNAs) as an emerging aspect of gene regulation. We used data mining to identify circRNAs and characterize their expression profiles within RNAseq data collected from thermally challenged turkey poults of the RBC2 and F-lines. From sequences of 28 paired-end libraries, 8924 unique circRNAs were predicted of which 1629 were common to all treatment groups. Expression analysis identified significant differentially expressed circRNAs (DECs) in comparisons between thermal treatments (41 DECs) and between genetic lines (117 DECs). No intersection was observed between the DECs and differentially expressed gene transcripts indicating that the DECs are not simply the result of expression changes in the parental genes. Comparative analyses based on the chicken microRNA (miRNA) database suggest potential interactions between turkey circRNAs and miRNAs. Additional studies are needed to reveal the functional significance of the predicted circRNAs and their role in muscle development in response to thermal challenge. The DECs identified in this study provide an important framework for future investigation.
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Affiliation(s)
- Kent M Reed
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Kristelle M Mendoza
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, United States
| | - Sandra G Velleman
- Department of Animal Sciences, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH, United States
| | - Gale M Strasburg
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, United States
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13
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Chakraborty S, Driscoll HE, Abrahante JE, Zhang F, Fisher RF, Harris JM. Salt Stress Enhances Early Symbiotic Gene Expression in Medicago truncatula and Induces a Stress-Specific Set of Rhizobium-Responsive Genes. Mol Plant Microbe Interact 2021; 34:904-921. [PMID: 33819071 PMCID: PMC8578154 DOI: 10.1094/mpmi-01-21-0019-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Salt stress is a major agricultural concern inhibiting not only plant growth but also the symbiotic association between legume roots and the soil bacteria rhizobia. This symbiotic association is initiated by a molecular dialogue between the two partners, leading to the activation of a signaling cascade in the legume host and, ultimately, the formation of nitrogen-fixing root nodules. Here, we show that a moderate salt stress increases the responsiveness of early symbiotic genes in Medicago truncatula to its symbiotic partner, Sinorhizobium meliloti while, conversely, inoculation with S. meliloti counteracts salt-regulated gene expression, restoring one-third to control levels. Our analysis of early nodulin 11 (ENOD11) shows that salt-induced expression is dynamic, Nod-factor dependent, and requires the ionic but not the osmotic component of salt. We demonstrate that salt stimulation of rhizobium-induced gene expression requires NSP2, which functions as a node to integrate the abiotic and biotic signals. In addition, our work reveals that inoculation with S. meliloti succinoglycan mutants also hyperinduces ENOD11 expression in the presence or absence of salt, suggesting a possible link between rhizobial exopolysaccharide and the plant response to salt stress. Finally, we identify an accessory set of genes that are induced by rhizobium only under conditions of salt stress and have not been previously identified as being nodulation-related genes. Our data suggest that interplay of core nodulation genes with different accessory sets, specific for different abiotic conditions, functions to establish the symbiosis. Together, our findings reveal a complex and dynamic interaction between plant, microbe, and environment.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Sanhita Chakraborty
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heather E. Driscoll
- Vermont Biomedical Research Network (VBRN), Department of Biology, Norwich University, Northfield, Vermont 05663, USA
| | - Juan E. Abrahante
- University of Minnesota Informatics Institute (UMII) (CCRB 1-210C), 2231 6th Street SE, Minneapolis, MN 55455, USA
| | - Fan Zhang
- Vermont Biomedical Research Network (VBRN), Department of Biology, University of Vermont, Burlington, Vermont 05405, USA
- Institute for Translational Research and Department of family medicine, University of North Texas Health Science Center, Fort Worth, TX, 76107
| | - Robert F. Fisher
- Stanford University, Department of Biology, 371 Serra Mall, Stanford, California 94305-5020, USA
| | - Jeanne M. Harris
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
- Corresponding author: Jeanne M. Harris ()
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14
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Tran PV, Johns ME, McAdams B, Abrahante JE, Simone DA, Banik RK. Global transcriptome analysis of rat dorsal root ganglia to identify molecular pathways involved in incisional pain. Mol Pain 2021; 16:1744806920956480. [PMID: 32909881 PMCID: PMC7493244 DOI: 10.1177/1744806920956480] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To develop non-opioid therapies for postoperative incisional pain, we must understand its underlying molecular mechanisms. In this study, we assessed global gene expression changes in dorsal root ganglia neurons in a model of incisional pain to identify pertinent molecular pathways. Male, Sprague-Dawley rats underwent infiltration of 1% capsaicin or vehicle into the plantar hind paw (n = 6-9/group) 30 min before plantar incision. Twenty-four hours after incision or sham (control) surgery, lumbar L4-L6 dorsal root ganglias were collected from rats pretreated with vehicle or capsaicin. RNA was isolated and sequenced by next generation sequencing. The genes were then annotated to functional networks using a knowledge-based database, Ingenuity Pathway Analysis. In rats pretreated with vehicle, plantar incision caused robust hyperalgesia, up-regulated 36 genes and downregulated 90 genes in dorsal root ganglias one day after plantar incision. Capsaicin pretreatment attenuated pain behaviors, caused localized denervation of the dermis and epidermis, and prevented the incision-induced changes in 99 of 126 genes. The pathway analyses showed altered gene networks related to increased pro-inflammatory and decreased anti-inflammatory responses in dorsal root ganglias. Insulin-like growth factor signaling was identified as one of the major gene networks involved in the development of incisional pain. Expression of insulin-like growth factor -2 and IGFBP6 in dorsal root ganglia were independently validated with quantitative real-time polymerase chain reaction. We discovered a distinct subset of dorsal root ganglia genes and three key signaling pathways that are altered 24 h after plantar incision but are unchanged when incision was made after capsaicin infiltration in the skin. Further exploration of molecular mechanisms of incisional pain may yield novel therapeutic targets.
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Affiliation(s)
- Phu V Tran
- Department of Pediatrics, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Malcolm E Johns
- Department of Anesthesiology, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Brian McAdams
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
| | - Juan E Abrahante
- Informatics Institute, University of Minnesota, Minneapolis, MN, USA
| | - Donald A Simone
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
| | - Ratan K Banik
- Department of Anesthesiology, School of Medicine, University of Minnesota, Minneapolis, MN, USA
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15
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Berkebile ZW, Putri DS, Abrahante JE, Seelig DM, Schleiss MR, Bierle CJ. The Placental Response to Guinea Pig Cytomegalovirus Depends Upon the Timing of Maternal Infection. Front Immunol 2021; 12:686415. [PMID: 34211475 PMCID: PMC8239309 DOI: 10.3389/fimmu.2021.686415] [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: 03/26/2021] [Accepted: 05/25/2021] [Indexed: 11/16/2022] Open
Abstract
Human cytomegalovirus (HCMV) infects the placenta, and these placental infections can cause fetal injury and/or demise. The timing of maternal HCMV infection during pregnancy is a determinant of fetal outcomes, but how development affects the placenta’s susceptibility to infection, the likelihood of placental injury post-infection, and the frequency of transplacental HCMV transmission remains unclear. In this study, guinea pig cytomegalovirus (GPCMV) was used to model primary maternal infection and compare the effects of infection at two different times on the placenta. When guinea pigs were infected with GPCMV at either 21- or 35-days gestation (dGA), maternal and placental viral loads, as determined by droplet digital PCR, were not significantly affected by the timing of maternal infection. However, when the transcriptomes of gestational age-matched GPCMV-infected and control placentas were compared, significant infection-associated changes in gene expression were only observed after maternal infection at 35 dGA. Notably, transcripts associated with immune activation (e.g. Cxcl10, Ido1, Tgtp1, and Tlr8) were upregulated in the infected placenta. A GPCMV-specific in situ hybridization assay detected rare infected cells in the main placenta after maternal infection at either time, and maternal infection at 35 dGA also caused large areas of GPCMV-infected cells in the junctional zone. As GPCMV infection after mid-gestation is known to cause high rates of stillbirth and/or fetal growth restriction, our results suggest that the placenta becomes sensitized to infection-associated injury late in gestation, conferring an increased risk of adverse pregnancy outcomes after cytomegalovirus infection.
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Affiliation(s)
- Zachary W Berkebile
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Minnesota, Minneapolis, MN, United States
| | - Dira S Putri
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Minnesota, Minneapolis, MN, United States
| | - Juan E Abrahante
- Informatics Institute, University of Minnesota, Minneapolis, MN, United States
| | - Davis M Seelig
- Department of Veterinary Clinical Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Mark R Schleiss
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Minnesota, Minneapolis, MN, United States
| | - Craig J Bierle
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Minnesota, Minneapolis, MN, United States
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16
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Lockridge A, Jo S, Gustafson E, Damberg N, Mohan R, Olson M, Abrahante JE, Alejandro EU. Islet O-GlcNAcylation Is Required for Lipid Potentiation of Insulin Secretion through SERCA2. Cell Rep 2021; 31:107609. [PMID: 32375037 DOI: 10.1016/j.celrep.2020.107609] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 01/24/2020] [Accepted: 04/12/2020] [Indexed: 12/19/2022] Open
Abstract
During early obesity, pancreatic β cells compensate for increased metabolic demand through a transient phase of insulin hypersecretion that stabilizes blood glucose and forestalls diabetic progression. We find evidence that β cell O-GlcNAcylation, a nutrient-responsive post-translational protein modification regulated by O-GlcNAc transferase (OGT), is critical for coupling hyperlipidemia to β cell functional adaptation during this compensatory prediabetic phase. In mice, islet O-GlcNAcylation rises and falls in tandem with the timeline of secretory potentiation during high-fat feeding while genetic models of β-cell-specific OGT loss abolish hyperinsulinemic responses to lipids, in vivo and in vitro. We identify the endoplasmic reticulum (ER) Ca2+ ATPase SERCA2 as a β cell O-GlcNAcylated protein in mice and humans that is able to rescue palmitate-stimulated insulin secretion through pharmacological activation. This study reveals an important physiological role for β cell O-GlcNAcylation in sensing and responding to obesity, with therapeutic implications for managing the relationship between type 2 diabetes and its most common risk factor.
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Affiliation(s)
- Amber Lockridge
- Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Seokwon Jo
- Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Eric Gustafson
- Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Niklas Damberg
- Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Ramkumar Mohan
- Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Miranda Olson
- Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Juan E Abrahante
- Supercomputing Institute, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Emilyn U Alejandro
- Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, USA.
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17
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Conboy CB, Vélez-Reyes GL, Rathe SK, Abrahante JE, Temiz NA, Burns MB, Harris RS, Starr TK, Largaespada DA. R-Spondins 2 and 3 Are Overexpressed in a Subset of Human Colon and Breast Cancers. DNA Cell Biol 2020; 40:70-79. [PMID: 33320737 DOI: 10.1089/dna.2020.5585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Wnt signaling is activated in many cancer types, yet targeting the canonical Wnt pathway has been challenging for cancer therapy. The pathway might be effectively targeted at many levels depending on the mechanism by which it has become hyperactive. Recently, mouse genetic screens have found that R-spondins (RSPOs) act as oncogenes. Evidence includes recurrent genomic rearrangements that led to increased RSPO2 or RSPO3 expression in human colorectal adenocarcinomas, exclusive of APC mutations. RSPOs modulate Wnt signaling to promote epithelial cell proliferation and survival. These secreted proteins modulate Wnt signaling by binding to G-coupled receptors LGR4/5/6, ultimately inhibiting frizzled membrane clearance by RNF43 and ZNRF3. They also exert their function independent of leucine-rich repeat-containing, G protein-coupled receptors (LGRs) by binding to ZNRF3 and RNF43. This results in increased β-catenin concentration that, after translocation to the nucleus, acts as a transcriptional coactivator of genes necessary for proliferation and cell survival. In this article, we aimed to identify the role of RSPOs in colon and breast cancers by using in silico and in vitro studies. We found that expression of RSPO2 and RSPO3 at high levels characterized a subset of colorectal cancers (CRCs). RSPO2 expression was found to characterize a subset of triple-negative breast cancers. In both instances, increased expression of RSPOs was associated with an activated Wnt signaling gene expression profile. Furthermore, knockdown of RSPO2 decreased Wnt signaling and proliferation in human breast cancer cells. Our findings show and confirm that RSPO2 and RSPO3 expression is upregulated in a subset of colorectal adenocarcinomas and breast cancers and that both are attractive druggable oncoprotein targets against such cancers. We also describe novel fusion transcripts that occur in CRC.
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Affiliation(s)
- Caitlin B Conboy
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Susan K Rathe
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, Minnesota, USA
| | - Nuri A Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael B Burns
- Biochemistry, Molecular Biology and Biophysics Department, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Reuben S Harris
- Biochemistry, Molecular Biology and Biophysics Department, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Timothy K Starr
- Department of Obstetrics, Gynecology and Women's Health and University of Minnesota, Minneapolis, Minnesota, USA
| | - David A Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
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18
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Crouse B, Robinson C, Huseby Kelcher A, Laudenbach M, Abrahante JE, Pravetoni M. Mechanisms of interleukin 4 mediated increase in efficacy of vaccines against opioid use disorders. NPJ Vaccines 2020; 5:99. [PMID: 33101712 PMCID: PMC7578047 DOI: 10.1038/s41541-020-00247-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 05/19/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022] Open
Abstract
Opioid use disorders (OUD) affect over 27 million people worldwide. Anti-opioid vaccines offer a promising strategy to treat OUD and prevent overdose. Using immunomodulation of cytokine signaling to increase vaccine efficacy, this study found that blocking IL-4 improved the efficacy of vaccines targeting oxycodone and fentanyl in male and female mice. Genetic deletion of the IL-4 receptor, STAT6, or antibody-based depletion of IL-13, did not increase vaccine efficacy against opioids, suggesting the involvement of type I IL-4 receptors. Enhancement of vaccine efficacy with blockade of IL-4 was associated with improved germinal center formation in secondary lymphoid organs and selective transcriptome signatures in the activated CD4+ T cell population subset. These data suggest that IL-4 is both a pharmacological target and a potential biomarker of vaccine efficacy against OUD.
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Affiliation(s)
- Bethany Crouse
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455 USA.,Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55455 USA
| | - Christine Robinson
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - April Huseby Kelcher
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455 USA.,Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Megan Laudenbach
- Hennepin Healthcare Research Institute, Minneapolis, MN 55404 USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN 55455 USA
| | - Marco Pravetoni
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455 USA.,Center for Immunology, University of Minnesota, Minneapolis, MN 55455 USA
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19
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Smeester BA, Draper GM, Slipek NJ, Larsson AT, Stratton N, Pomeroy EJ, Becklin KL, Yamamoto K, Williams KB, Laoharawee K, Peterson JJ, Abrahante JE, Rathe SK, Mills LJ, Crosby MR, Hudson WA, Rahrmann EP, Largaespada DA, Moriarity BS. Implication of ZNF217 in Accelerating Tumor Development and Therapeutically Targeting ZNF217-Induced PI3K-AKT Signaling for the Treatment of Metastatic Osteosarcoma. Mol Cancer Ther 2020; 19:2528-2541. [PMID: 32999043 DOI: 10.1158/1535-7163.mct-20-0369] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/15/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022]
Abstract
We previously identified ZNF217 as an oncogenic driver of a subset of osteosarcomas using the Sleeping Beauty (SB) transposon system. Here, we followed up by investigating the genetic role of ZNF217 in osteosarcoma initiation and progression through the establishment of a novel genetically engineered mouse model, in vitro assays, orthotopic mouse studies, and paired these findings with preclinical studies using a small-molecule inhibitor. Throughout, we demonstrate that ZNF217 is coupled to numerous facets of osteosarcoma transformation, including proliferation, cell motility, and anchorage independent growth, and ultimately promoting osteosarcoma growth, progression, and metastasis in part through positive modulation of PI3K-AKT survival signaling. Pharmacologic blockade of AKT signaling with nucleoside analogue triciribine in ZNF217+ orthotopically injected osteosarcoma cell lines reduced tumor growth and metastasis. Our data demonstrate that triciribine treatment may be a relevant and efficacious therapeutic strategy for patients with osteosarcoma with ZNF217+ and p-AKT rich tumors. With the recent revitalization of triciribine for clinical studies in other solid cancers, our study provides a rationale for further evaluation preclinically with the purpose of clinical evaluation in patients with incurable, ZNF217+ osteosarcoma.
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Affiliation(s)
- Branden A Smeester
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Garrett M Draper
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Nicholas J Slipek
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Alex T Larsson
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Natalie Stratton
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Emily J Pomeroy
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Kelsie L Becklin
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Kenta Yamamoto
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Kyle B Williams
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Kanut Laoharawee
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Joseph J Peterson
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | | | - Susan K Rathe
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Lauren J Mills
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Margaret R Crosby
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Wendy A Hudson
- AHCSH Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Eric P Rahrmann
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, England
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20
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Sariol A, Mackin S, Allred MG, Ma C, Zhou Y, Zhang Q, Zou X, Abrahante JE, Meyerholz DK, Perlman S. Microglia depletion exacerbates demyelination and impairs remyelination in a neurotropic coronavirus infection. Proc Natl Acad Sci U S A 2020; 117:24464-24474. [PMID: 32929007 PMCID: PMC7533697 DOI: 10.1073/pnas.2007814117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [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: 12/21/2022] Open
Abstract
Microglia are considered both pathogenic and protective during recovery from demyelination, but their precise role remains ill defined. Here, using an inhibitor of colony stimulating factor 1 receptor (CSF1R), PLX5622, and mice infected with a neurotropic coronavirus (mouse hepatitis virus [MHV], strain JHMV), we show that depletion of microglia during the time of JHMV clearance resulted in impaired myelin repair and prolonged clinical disease without affecting the kinetics of virus clearance. Microglia were required only during the early stages of remyelination. Notably, large deposits of extracellular vesiculated myelin and cellular debris were detected in the spinal cords of PLX5622-treated and not control mice, which correlated with decreased numbers of oligodendrocytes in demyelinating lesions in drug-treated mice. Furthermore, gene expression analyses demonstrated differential expression of genes involved in myelin debris clearance, lipid and cholesterol recycling, and promotion of oligodendrocyte function. The results also demonstrate that microglial functions affected by depletion could not be compensated by infiltrating macrophages. Together, these results demonstrate that microglia play key roles in debris clearance and in the initiation of remyelination following infection with a neurotropic coronavirus but are not necessary during later stages of remyelination.
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Affiliation(s)
- Alan Sariol
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA 52242
| | - Samantha Mackin
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
| | - Merri-Grace Allred
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA 52242
| | - Chen Ma
- School of Mathematics and Statistics, Wuhan University, 430072 Wuhan, China
| | - Yu Zhou
- School of Mathematics and Statistics, Wuhan University, 430072 Wuhan, China
| | - Qinran Zhang
- School of Mathematics and Statistics, Wuhan University, 430072 Wuhan, China
| | - Xiufen Zou
- School of Mathematics and Statistics, Wuhan University, 430072 Wuhan, China
| | - Juan E Abrahante
- University of Minnesota Informatics Institute (UMII), Minneapolis, MN 55455
| | | | - Stanley Perlman
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA 52242;
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
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21
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Putri DS, Berkebile ZW, Mustafa HJ, Fernández-Alarcón C, Abrahante JE, Schleiss MR, Bierle CJ. Cytomegalovirus infection elicits a conserved chemokine response from human and guinea pig amnion cells. Virology 2020; 548:93-100. [PMID: 32838950 DOI: 10.1016/j.virol.2020.06.005] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 02/06/2023]
Abstract
Human cytomegalovirus (HCMV) infects the chorioamnion, but whether these infections cause fetal membrane dysfunction remains poorly understood. We sought to assess whether guinea pig cytomegalovirus (GPCMV) infects amnion-derived cells in vitro, compare the inflammatory response of amnion cells to GPCMV and HCMV, and determine if GPCMV infects the amnion in vivo. We found that GPCMV replicates in primary guinea pig amnion derived cells and HPV16 E6/E7-transduced amniotic epithelial cells (AEC[E6/E7]s). HCMV and GPCMV infection of amnion cells increased the transcription of the chemokines CCL5/Ccl5, CXCL8/Cxcl8, and CXCL10/Cxcl10. Myd88-knockdown decreased Ccl5 and Cxc8 transcription in GPCMV-infected AEC[E6/E7]s. GPCMV was detected in the guinea pig amnion after primary maternal infection, revealing that guinea pigs are an appropriate model to study fetal membrane physiology after cytomegalovirus infection. As inflammation is known to cause fetal membrane weakening, the amnion's response to cytomegalovirus infection may cause preterm birth and other adverse pregnancy outcomes.
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Affiliation(s)
- Dira S Putri
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, MN, USA.
| | - Zachary W Berkebile
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, MN, USA.
| | - Hiba J Mustafa
- Department of Obstetrics, Gynecology and Women's Health, Division of Maternal-Fetal Medicine, University of Minnesota, Minneapolis, MN, USA.
| | - Claudia Fernández-Alarcón
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, MN, USA.
| | - Juan E Abrahante
- Informatics Institute, University of Minnesota, Minneapolis, MN, USA.
| | - Mark R Schleiss
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, MN, USA.
| | - Craig J Bierle
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, MN, USA.
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22
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Taylor RM, Mendoza KM, Abrahante JE, Reed KM, Sunde RA. The hepatic transcriptome of the turkey poult (Meleagris gallopavo) is minimally altered by high inorganic dietary selenium. PLoS One 2020; 15:e0232160. [PMID: 32379770 PMCID: PMC7205448 DOI: 10.1371/journal.pone.0232160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/08/2020] [Indexed: 12/18/2022] Open
Abstract
There is interest in supplementing animals and humans with selenium (Se) above Se-adequate levels, but the only good biomarker for toxicity is tissue Se. We targeted liver because turkeys fed 5 μg Se/g have hepatic Se concentrations 6-fold above Se-adequate (0.4 μg Se/g) levels without effects on growth or health. Our objectives were (i) to identify transcript biomarkers for high Se status, which in turn would (ii) suggest proteins and pathways used by animals to adapt to high Se. Turkey poults were fed 0, 0.025, 0.4, 0.75 and 1.0 μg Se/g diet in experiment 1, and fed 0.4, 2.0 and 5.0 μg Se/g in experiment 2, as selenite, and the full liver transcriptome determined by RNA-Seq. The major effect of Se-deficiency was to down-regulate expression of a subset of selenoprotein transcripts, with little significant effect on general transcript expression. In response to high Se intake (2 and 5 μg Se/g) relative to Se-adequate turkeys, there were only a limited number of significant differentially expressed transcripts, all with only relatively small fold-changes. No transcript showed a consistent pattern of altered expression in response to high Se intakes across the 1, 2 and 5 μg Se/g treatments, and there were no associated metabolic pathways and biological functions that were significant and consistently found with high Se supplementation. Gene set enrichment analysis also found no gene sets that were consistently altered by high-Se and supernutritional-Se. A comparison of differentially expressed transcript sets with high Se transcript sets identified in mice provided high Se (~3 μg Se/g) also failed to identify common differentially expressed transcript sets between these two species. Collectively, this study indicates that turkeys do not alter gene expression in the liver as a homeostatic mechanism to adapt to high Se.
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Affiliation(s)
- Rachel M. Taylor
- Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kristelle M. Mendoza
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Juan E. Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Kent M. Reed
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Roger A. Sunde
- Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
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23
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Vidovic S, Liu X, An R, Mendoza KM, Abrahante JE, Johny AK, Reed KM. Transcriptional Profiling and Molecular Characterization of the yccT Mutant Link: A Novel STY1099 Protein with the Peroxide Stress Response and Cell Division of Salmonella enterica Serovar Enteritidis. Biology (Basel) 2019; 8:biology8040086. [PMID: 31766267 PMCID: PMC6955953 DOI: 10.3390/biology8040086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 11/16/2022]
Abstract
Uncharacterized protein STY1099, encoded by the yccT gene, was previously identified as the most altered (i.e., upregulated) protein among the ZnO nanoparticle (NP) stimulon of Salmonella enterica serovar Enteritidis. Here we combined various stress response-related assays with functional genetics, global transcriptomic and proteomic analyses to characterize the yccT gene and its STY1099 product. Exposure of S. enterica Enteritidis to H2O2 (i.e., hydrogen peroxide) resulted in a significant (p < 0.0001) upregulation of the yccT gene, whereas exposure to paraquat (i.e., superoxide) did not alter the expression of the yccT gene. The ∆yccT mutant of S. enterica Enteritidis exposed to 0.75 mM H2O2, showed significantly reduced (p < 0.05) viability compared to the wild type strain. Further, comparative transcriptome analyses supported by Co-immunoprecipitation (Co-IP) assay revealed that STY1099 protein plays a role in redox homeostasis during the peroxide stress assault via involvement in the processes of respiratory nitrate reductase, oxidoreductase activities, cellular uptake and stress response. In addition, we found that the STY1099 protein has the monopolar subcellular location and that it interacts with key cell division proteins, MinD, and FtsH, as well as with a rod shape-determining protein MerB.
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Affiliation(s)
- Sinisa Vidovic
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (X.L.); (R.A.); (K.M.M.); (K.M.R.)
- Correspondence: ; Tel.: +1-612-626-3669
| | - Xiaoying Liu
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (X.L.); (R.A.); (K.M.M.); (K.M.R.)
| | - Ran An
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (X.L.); (R.A.); (K.M.M.); (K.M.R.)
| | - Kristelle M. Mendoza
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (X.L.); (R.A.); (K.M.M.); (K.M.R.)
| | - Juan E. Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Anup K. Johny
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA;
| | - Kent M. Reed
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (X.L.); (R.A.); (K.M.M.); (K.M.R.)
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24
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Conboy CB, Vélez-Reyes GL, Tschida BR, Hu H, Kaufmann G, Koes N, Keller B, Alsinet C, Cornellà H, Pinyol R, Abrahante JE, Temiz NA, Linden MA, Amin K, Kuka TP, Keng VW, Llovet JM, Starr TK, Largaespada DA. R-spondin 2 Drives Liver Tumor Development in a Yes-Associated Protein-Dependent Manner. Hepatol Commun 2019; 3:1496-1509. [PMID: 31701073 PMCID: PMC6824083 DOI: 10.1002/hep4.1422] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/10/2019] [Indexed: 12/17/2022] Open
Abstract
Each year, more than 25,000 people succumb to liver cancer in the United States, and this neoplasm represents the second cause of cancer-related death globally. R-spondins (RSPOs) are secreted regulators of Wnt signaling that function in development and promote tissue stem cell renewal. In cancer, RSPOs 2 and 3 are oncogenes first identified by insertional mutagenesis screens in tumors induced by mouse mammary tumor virus and by transposon mutagenesis in the colonic epithelium of rodents. RSPO2 has been reported to be activated by chromosomal rearrangements in colorectal cancer and overexpressed in a subset of hepatocellular carcinoma. Using human liver tumor gene expression data, we first discovered that a subset of liver cancers were characterized by high levels of RSPO2 in contrast to low levels in adjacent nontumor tissue. To determine if RSPOs are capable of inducing liver tumors, we used an in vivo model from which we found that overexpression of RSPO2 in the liver promoted Wnt signaling, hepatomegaly, and enhanced liver tumor formation when combined with loss of transformation-related protein 53 (Trp53). Moreover, the Hippo/yes-associated protein (Yap) pathway has been implicated in many human cancers, influencing cell survival. Histologic and gene expression studies showed activation of Wnt/β-catenin and Hippo/Yap pathways following RSPO2 overexpression. We demonstrate that knockdown of Yap1 leads to reduced tumor penetrance following RSPO2 overexpression in the context of loss of Trp53. Conclusion: RSPO2 overexpression leads to tumor formation in the mouse liver in a Hippo/Yap-dependent manner. Overall, our results suggest a role for Yap in the initiation and progression of liver tumors and uncover a novel pathway activated in RSPO2-induced malignancies. We show that RSPO2 promotes liver tumor formation in vivo and in vitro and that RSPO2's oncogenic activity requires Hippo/Yap activation in hepatocytes. Both RSPO2 and YAP1 are suggested to represent novel druggable targets in Wnt-driven tumors of the liver.
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Affiliation(s)
| | | | | | - Hsiangyu Hu
- Masonic Cancer Center University of Minnesota Minneapolis MN
| | | | - Nicholas Koes
- Masonic Cancer Center University of Minnesota Minneapolis MN
| | - Bryant Keller
- Masonic Cancer Center University of Minnesota Minneapolis MN
| | - Clara Alsinet
- Liver Cancer Translational Research Laboratory Liver Unit, L'Institut d'Investigacions Biomèdiques August Pi i Sunyer-Hospital Clinic of Barcelona University of Barcelona Barcelona Spain
| | - Helena Cornellà
- Liver Cancer Translational Research Laboratory Liver Unit, L'Institut d'Investigacions Biomèdiques August Pi i Sunyer-Hospital Clinic of Barcelona University of Barcelona Barcelona Spain
| | - Roser Pinyol
- Liver Cancer Translational Research Laboratory Liver Unit, L'Institut d'Investigacions Biomèdiques August Pi i Sunyer-Hospital Clinic of Barcelona University of Barcelona Barcelona Spain
| | | | - Nuri A Temiz
- Masonic Cancer Center University of Minnesota Minneapolis MN
| | - Michael A Linden
- Comparative Pathology Shared Resource University of Minnesota St. Paul MN.,Department of Medicine Division of Hematology, Oncology, and Transplantation University of Minnesota Minneapolis MN
| | - Khalid Amin
- Comparative Pathology Shared Resource University of Minnesota St. Paul MN.,Department of Medicine Division of Hematology, Oncology, and Transplantation University of Minnesota Minneapolis MN
| | - Timothy P Kuka
- Masonic Cancer Center University of Minnesota Minneapolis MN
| | - Vincent W Keng
- Masonic Cancer Center University of Minnesota Minneapolis MN.,Department of Applied Biology and Chemical Technology Hong Kong Polytechnic University Kowloon Hong Kong
| | - Josep M Llovet
- Liver Cancer Translational Research Laboratory Liver Unit, L'Institut d'Investigacions Biomèdiques August Pi i Sunyer-Hospital Clinic of Barcelona University of Barcelona Barcelona Spain.,Mount Sinai Liver Cancer Program Division of Liver Diseases Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai New York NY.,Catalan Institution for Research and Advanced Studies Barcelona Spain
| | - Timothy K Starr
- Department of Obstetrics, Gynecology, and Women's Health University of Minnesota Minneapolis MN
| | - David A Largaespada
- Masonic Cancer Center University of Minnesota Minneapolis MN.,Department of Pediatrics University of Minnesota Minneapolis MN
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25
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Singh A, Ramachandran S, Graham ML, Daneshmandi S, Heller D, Suarez-Pinzon WL, Balamurugan AN, Ansite JD, Wilhelm JJ, Yang A, Zhang Y, Palani NP, Abrahante JE, Burlak C, Miller SD, Luo X, Hering BJ. Long-term tolerance of islet allografts in nonhuman primates induced by apoptotic donor leukocytes. Nat Commun 2019; 10:3495. [PMID: 31375697 PMCID: PMC6677762 DOI: 10.1038/s41467-019-11338-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 11/28/2018] [Accepted: 07/09/2019] [Indexed: 02/06/2023] Open
Abstract
Immune tolerance to allografts has been pursued for decades as an important goal in transplantation. Administration of apoptotic donor splenocytes effectively induces antigen-specific tolerance to allografts in murine studies. Here we show that two peritransplant infusions of apoptotic donor leukocytes under short-term immunotherapy with antagonistic anti-CD40 antibody 2C10R4, rapamycin, soluble tumor necrosis factor receptor and anti-interleukin 6 receptor antibody induce long-term (≥1 year) tolerance to islet allografts in 5 of 5 nonsensitized, MHC class I-disparate, and one MHC class II DRB allele-matched rhesus macaques. Tolerance in our preclinical model is associated with a regulatory network, involving antigen-specific Tr1 cells exhibiting a distinct transcriptome and indirect specificity for matched MHC class II and mismatched class I peptides. Apoptotic donor leukocyte infusions warrant continued investigation as a cellular, nonchimeric and translatable method for inducing antigen-specific tolerance in transplantation. Injection of donor apoptotic cells induces graft tolerance in mice. Here the authors combine this approach with short immunosuppressive therapy to achieve long-term tolerance to allogeneic islets and restoration of normoglycemia in diabetic nonhuman primates, and delineate cellular and molecular correlates of tolerance induction.
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Affiliation(s)
- Amar Singh
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Sabarinathan Ramachandran
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Melanie L Graham
- Preclinical Research Center, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Saeed Daneshmandi
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - David Heller
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wilma Lucia Suarez-Pinzon
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Appakalai N Balamurugan
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA.,Center for Cellular Transplantation, Cardiovascular Innovation Institute, Department of Surgery, University of Louisville, Louisville, KY, 40202, USA
| | - Jeffrey D Ansite
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joshua J Wilhelm
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Amy Yang
- Biostatistics Collaboration Center, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Ying Zhang
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Nagendra P Palani
- University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN, 55455, USA
| | - Christopher Burlak
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Stephen D Miller
- Department of Microbiology-Immunology and Interdepartmental Immunology Center, Northwestern University, Chicago, IL, 60611, USA.
| | - Xunrong Luo
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Biostatistics Collaboration Center, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Duke Transplant Center, Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Bernhard J Hering
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA.
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26
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Channappanavar R, Fehr AR, Zheng J, Wohlford-Lenane C, Abrahante JE, Mack M, Sompallae R, McCray PB, Meyerholz DK, Perlman S. IFN-I response timing relative to virus replication determines MERS coronavirus infection outcomes. J Clin Invest 2019; 129:3625-3639. [PMID: 31355779 DOI: 10.1172/jci126363] [Citation(s) in RCA: 399] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
Type 1 IFNs (IFN-I) generally protect mammalian hosts from virus infections, but in some cases, IFN-I is pathogenic. Because IFN-I is protective, it is commonly used to treat virus infections for which no specific approved drug or vaccine is available. The Middle East respiratory syndrome-coronavirus (MERS-CoV) is such an infection, yet little is known about the role of IFN-I in this setting. Here, we show that IFN-I signaling is protective during MERS-CoV infection. Blocking IFN-I signaling resulted in delayed virus clearance, enhanced neutrophil infiltration, and impaired MERS-CoV-specific T cell responses. Notably, IFN-I administration within 1 day after infection (before virus titers peak) protected mice from lethal infection, despite a decrease in IFN-stimulated gene (ISG) and inflammatory cytokine gene expression. In contrast, delayed IFN-β treatment failed to effectively inhibit virus replication, increased infiltration and activation of monocytes, macrophages, and neutrophils in the lungs, and enhanced proinflammatory cytokine expression, resulting in fatal pneumonia in an otherwise sublethal infection. Together, these results suggest that the relative timing of the IFN-I response and maximal virus replication is key in determining outcomes, at least in infected mice. By extension, IFN-αβ or combination therapy may need to be used cautiously to treat viral infections in clinical settings.
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Affiliation(s)
- Rudragouda Channappanavar
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA.,Department of Acute and Tertiary Care, and.,Department of Microbiology and Immunology, University of Tennessee Health Sciences Center, Memphis, Tennessee, USA
| | - Anthony R Fehr
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Jian Zheng
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | | | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Matthias Mack
- Department of Internal Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Paul B McCray
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA.,Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | | | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA.,Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA.,State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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27
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Seiler CL, Song JM, Fernandez J, Abrahante JE, Kono TJY, Chen Y, Ren Y, Kassie F, Tretyakova NY. Epigenetic Changes in Alveolar Type II Lung Cells of A/J Mice Following Intranasal Treatment with Lipopolysaccharide. Chem Res Toxicol 2019; 32:831-839. [PMID: 30942577 DOI: 10.1021/acs.chemrestox.9b00015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lipopolysaccharide (LPS) is a bacterial endotoxin present in cigarette smoke. LPS is known to induce inflammation and to increase the size and the multiplicity of lung tumors induced by tobacco-specific nitrosamines. However, the means by which LPS contributes to pulmonary carcinogenesis are not known. One possible mechanism includes LPS-mediated epigenetic deregulation, which leads to aberrant expression of genes involved in DNA repair, tumor suppression, cell cycle progression, and cell growth. In the present work, epigenetic effects of LPS were examined in alveolar type II lung cells of A/J mice. Type II cells were selected because they serve as progenitors of lung adenocarcinomas in smoking induced lung cancer. A/J mice were intranasally treated with LPS, followed by isolation of alveolar type II cells from the lung using cell panning. Global levels of DNA methylation and histone acetylation were quantified by mass spectrometry, while genome-wide transcriptomic changes were characterized by RNA-Seq. LPS treatment was associated with epigenetic changes including decreased cytosine formylation and reduced histone H3K14 and H3K23 acetylation, as well as altered expression levels of genes involved in cell adhesion, inflammation, immune response, and epigenetic regulation. These results suggest that exposure to inflammatory agents in cigarette smoke leads to early epigenetic changes in the lung, which may collaborate with genetic changes to drive the development of lung cancer.
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28
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Winterhoff BJ, Maile M, Mitra AK, Sebe A, Bazzaro M, Geller MA, Abrahante JE, Klein M, Hellweg R, Mullany SA, Beckman K, Daniel J, Starr TK. Corrigendum to "Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells" [Gyncol. Oncol. 144 (2017) 598-606]. Gynecol Oncol 2018; 151:182-186. [PMID: 30097329 DOI: 10.1016/j.ygyno.2018.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Boris J Winterhoff
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Makayla Maile
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Amit Kumar Mitra
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN, USA
| | - Attila Sebe
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Martina Bazzaro
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Melissa A Geller
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, USA
| | - Molly Klein
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Raffaele Hellweg
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA
| | - Sally A Mullany
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA
| | - Kenneth Beckman
- Genomics Center, University of Minnesota, Minneapolis, MN, USA
| | - Jerry Daniel
- Genomics Center, University of Minnesota, Minneapolis, MN, USA
| | - Timothy K Starr
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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29
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Winterhoff BJ, Clark CR, Ramesh S, Shetty M, Uppendahl L, Mitra AK, Sebe A, Bazzaro M, Geller MA, Abrahante JE, Molly K, Hellweg R, Mullany S, Beckman K, Daniel J, Starr TK. Abstract B59: Single-cell sequencing as a prognostic and predictive tool for ovarian cancer therapy. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.ovca17-b59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Technological advances allow genomic and transcriptomic analyses to be conducted at the single-cell level. Analysis of gene expression and DNA sequence at this detailed level could lead to prognostic and predictive biomarkers as well as an enhanced understanding of cancer cell and stromal subpopulations including stem cells and chemotherapy-resistant populations. This knowledge will improve our ability to implement a “precision medicine” approach to the treatment of women with ovarian cancer.
We have initiated a project to prospectively study the transcriptome and DNA exome of freshly isolated, high-grade serous ovarian cancer solid tumor samples at the single-cell level. To date we have enrolled 8 patients and have initiated single-cell whole-exome DNA sequencing, using the Fluidigm C1 chip, and single-cell whole-transcriptome RNA sequencing, using the 10X Genomics platform. For comparison of RNA sequencing technologies, we previously performed RNA sequencing of a patient’s sample using the Fluidigm C1 chip. In addition to sequencing the primary tumor samples, we are concurrently attempting to establish patient-derived xenografts (PDXs) and cell lines for each patient. We have successfully generated PDX mice from the first patient and are currently treating a subset of the mice with carboplatin/paclitaxel. Patients will be followed prospectively and information on their clinical response will be incorporated into the analysis.
Analysis of the RNA sequencing results from the first patient using the Fluidigm C1 platform identified several distinct populations of cells characterized by gene expression patterns that correlate with specific signaling pathways and disease states. We could clearly differentiate stromal cells from cancer epithelial cells based on gene expression patterns. Furthermore, using known functional markers, we could define subsets within each population, including three subgroups of cancer cells and four subgroups of stromal cells. Based on their gene expression patterns, we could determine the frequency of cancer epithelial cells compared to cancer cells undergoing epithelial-to-mesenchymal transition, as well as activated and nonactivated fibroblasts and myofibroblasts. We were also able to identify rare cells expressing stem cell markers.
Using the 10X Genomics platform, we have completed RNA sequencing of five patients (~370 million reads/patient). We quantified gene expression on an average of 8,707 cells/patient and 1,723 genes/cell. Using graph-based clustering combined with the t-Distributed Stochastic Neighbor Embedding technique for high dimensionality reduction, we have identified approximately 9 to 15 subsets of cells within these cancer samples based on an unbiased analysis of their gene expression patterns. Using bioinformatic tools, including CellRanger, Seurat, Ingenuity Pathway Analysis, and Gene Set Enrichment Analysis, we can define several of these subsets based on known functional markers, including subsets of immune cells, stromal cells, and cancer epithelial cells. We can estimate the frequency of each subset and can also subdivide the groups using cell-type specific markers, for example, by distinguishing macrophages from dendritic cells within the immune subset.
We will present unpublished data, including RNA sequencing and DNA exome sequencing of single cells on the first 8 enrolled patients. In addition to sequencing the primary tumor samples, we plan on performing single-cell sequencing of matched platinum-resistant tumors generated by treating the PDX mice with carboplatin and paclitaxel. We will also correlate presence and percentage of cell subpopulations with clinical outcomes of the patients. Our long-term goal is to use single-cell data as a prognostic biomarker for chemotherapy resistance as well as a tool for predicting effective therapeutic options, including targeted therapy and immune therapy.
Citation Format: Boris J. Winterhoff, Christopher R. Clark, Sidharth Ramesh, Mihir Shetty, Locke Uppendahl, Amit Kumra Mitra, Attila Sebe, Martina Bazzaro, Melissa A. Geller, Juan E. Abrahante, Klein Molly, Raffaele Hellweg, Sally Mullany, Kenneth Beckman, Jerry Daniel, Timothy K. Starr. Single-cell sequencing as a prognostic and predictive tool for ovarian cancer therapy. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B59.
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Kluesner MG, Nedveck DA, Lahr WS, Garbe JR, Abrahante JE, Webber BR, Moriarity BS. EditR: A Method to Quantify Base Editing from Sanger Sequencing. CRISPR J 2018; 1:239-250. [PMID: 31021262 PMCID: PMC6694769 DOI: 10.1089/crispr.2018.0014] [Citation(s) in RCA: 250] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9-Cytidine deaminase fusion enzymes—termed “base editors”—allow targeted editing of genomic deoxycytidine to deoxythymidine (C:G→T:A) without the need for double-stranded break induction. Base editors represent a paradigm shift in gene editing technology due to their unprecedented efficiency to mediate targeted, single-base conversion. However, current analysis of base editing outcomes rely on methods that are either imprecise or expensive and time-consuming. To overcome these limitations, we developed a simple, cost-effective, and accurate program to measure base editing efficiency from fluorescence-based Sanger sequencing, termed “EditR.” We provide EditR as a free online tool or downloadable desktop application requiring a single Sanger sequencing file and guide RNA sequence. EditR is more accurate than enzymatic assays, and provides added insight to the position, type, and efficiency of base editing. Furthermore, EditR is likely amenable to quantify base editing from the recently developed adenosine deaminase base editors that act on either DNA (adenosine deaminase base editors [ABEs]) or RNA (REPAIRs) (catalyzes A:T→G:C). Collectively, we demonstrate that EditR is a robust, inexpensive tool that will facilitate the broad application of base editing technology, thereby fostering further innovation in this burgeoning field.
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Affiliation(s)
- Mitchell G Kluesner
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
| | - Derek A Nedveck
- 4 Department of Plant Biology, University of Minnesota , Minneapolis, Minnesota
| | - Walker S Lahr
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
| | - John R Garbe
- 5 Genomics Center, University of Minnesota , Minneapolis, Minnesota
| | - Juan E Abrahante
- 6 Informatics Institute, University of Minnesota , Minneapolis, Minnesota
| | - Beau R Webber
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
| | - Branden S Moriarity
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
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Reed KM, Mendoza KM, Abrahante JE, Coulombe RA. Comparative Response of the Hepatic Transcriptomes of Domesticated and Wild Turkey to Aflatoxin B₁. Toxins (Basel) 2018; 10:toxins10010042. [PMID: 29342849 PMCID: PMC5793129 DOI: 10.3390/toxins10010042] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/15/2022] Open
Abstract
The food-borne mycotoxin aflatoxin B1 (AFB1) poses a significant risk to poultry, which are highly susceptible to its hepatotoxic effects. Domesticated turkeys (Meleagris gallopavo) are especially sensitive, whereas wild turkeys (M. g. silvestris) are more resistant. AFB1 toxicity entails bioactivation by hepatic cytochrome P450s to the electrophilic exo-AFB1-8,9-epoxide (AFBO). Domesticated turkeys lack functional hepatic GST-mediated detoxification of AFBO, and this is largely responsible for the differences in resistance between turkey types. This study was designed to characterize transcriptional changes induced in turkey livers by AFB1, and to contrast the response of domesticated (susceptible) and wild (more resistant) birds. Gene expression responses to AFB1 were examined using RNA-sequencing. Statistically significant differences in gene expression were observed among treatment groups and between turkey types. Expression analysis identified 4621 genes with significant differential expression (DE) in AFB1-treated birds compared to controls. Characterization of DE transcripts revealed genes dis-regulated in response to toxic insult with significant association of Phase I and Phase II genes and others important in cellular regulation, modulation of apoptosis, and inflammatory responses. Constitutive expression of GSTA3 was significantly higher in wild birds and was significantly higher in AFB1-treated birds when compared to controls for both genetic groups. This pattern was also observed by qRT-PCR in other wild and domesticated turkey strains. Results of this study emphasize the differential response of these genetically distinct birds, and identify genes and pathways that are differentially altered in aflatoxicosis.
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Affiliation(s)
- Kent M Reed
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Kristelle M Mendoza
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Roger A Coulombe
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture, Utah State University, Logan, UT 84322, USA.
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Angelos MG, Abrahante JE, Blum RH, Kaufman DS. Single Cell Resolution of Human Hematoendothelial Cells Defines Transcriptional Signatures of Hemogenic Endothelium. Stem Cells 2017; 36:206-217. [PMID: 29139170 DOI: 10.1002/stem.2739] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 10/20/2017] [Accepted: 11/04/2017] [Indexed: 12/20/2022]
Abstract
Endothelial-to-hematopoietic transition (EHT) is an important stage in definitive hematopoietic development. However, the genetic mechanisms underlying human EHT remain poorly characterized. We performed single cell RNA-seq using 55 hemogenic endothelial cells (HECs: CD31+ CD144+ CD41- CD43- CD45- CD73- RUNX1c+ ), 47 vascular endothelial cells without hematopoietic potential (non-HE: CD31+ CD144+ CD41- CD43- CD45- CD73- RUNX1c- ), and 35 hematopoietic progenitor cells (HPCs: CD34+ CD43+ RUNX1c+ ) derived from human embryonic stem cells (hESCs). HE and HP were enriched in genes implicated in hemogenic endothelial transcriptional networks, such as ERG, GATA2, and FLI. We found transcriptional overlap between individual HECs and HPCs; however, these populations were distinct from non-HE. Further analysis revealed novel biomarkers for human HEC/HPCs, including TIMP3, ESAM, RHOJ, and DLL4. Collectively, we demonstrate that hESC-derived HE and HP share a common developmental pathway, while non-HE are more heterogeneous and transcriptionally distinct. Our findings provide a novel strategy to test new genetic targets and optimize the production of definitive hematopoietic cells from human pluripotent stem cells. Stem Cells 2018;36:206-217.
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Affiliation(s)
- Mathew G Angelos
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, Minnesota, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, USA.,Medical Scientist Training Program, University of Minnesota, Minneapolis, Minnesota, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Robert H Blum
- Division of Regenerative Medicine, Department of Medicine, University of California-San Diego, La Jolla, California, USA
| | - Dan S Kaufman
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, Minnesota, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, USA.,Division of Regenerative Medicine, Department of Medicine, University of California-San Diego, La Jolla, California, USA
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Zhou K, Diebel KW, Holy J, Skildum A, Odean E, Hicks DA, Schotl B, Abrahante JE, Spillman MA, Bemis LT. A tRNA fragment, tRF5-Glu, regulates BCAR3 expression and proliferation in ovarian cancer cells. Oncotarget 2017; 8:95377-95391. [PMID: 29221134 PMCID: PMC5707028 DOI: 10.18632/oncotarget.20709] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/31/2017] [Indexed: 12/28/2022] Open
Abstract
Ovarian cancer is a complex disease marked by tumor heterogeneity, which contributes to difficulties in diagnosis and treatment. New molecular targets and better molecular profiles defining subsets of patients are needed. tRNA fragments (tRFs) offer a recently identified group of noncoding RNAs that are often as abundant as microRNAs in cancer cells. Initially their presence in deep sequencing data sets was attributed to the breakdown of mature tRNAs, however, it is now clear that they are actively generated and function in multiple regulatory events. One such tRF, a 5’ fragment of tRNA-Glu-CTC (tRF5-Glu), is processed from the mature tRNA-Glu and is shown in this study to be expressed in ovarian cancer cells. We confirmed that tRF5-Glu binds directly to a site in the 3’UTR of the Breast Cancer Anti-Estrogen Resistance 3 (BCAR3) mRNA thereby down regulating its expression. BCAR3 has not previously been studied in ovarian cancer cells and our studies demonstrate that inhibiting BCAR3 expression suppresses ovarian cancer cell proliferation. Furthermore, mimics of tRF5-Glu were found to inhibit proliferation of ovarian cancer cells. In summary, BCAR3 and tRF5-Glu contribute to the complex tumor heterogeneity of ovarian cancer cells and may provide new targets for therapeutic intervention.
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Affiliation(s)
- Kun Zhou
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Kevin W Diebel
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Jon Holy
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Andrew Skildum
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Evan Odean
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Douglas A Hicks
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Brent Schotl
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Monique A Spillman
- Texas A&M University Medical School, Baylor University Medical Center, Dallas, TX, 75206 USA
| | - Lynne T Bemis
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
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Paul JA, Aich A, Abrahante JE, Wang Y, LaRue RS, Rathe SK, Kalland K, Mittal A, Jha R, Peng F, Largaespada DA, Bagchi A, Gupta K. Transcriptomic analysis of gene signatures associated with sickle pain. Sci Data 2017; 4:170051. [PMID: 29292796 PMCID: PMC5749120 DOI: 10.1038/sdata.2017.51] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 10/04/2016] [Accepted: 03/02/2017] [Indexed: 01/17/2023] Open
Abstract
Pain is a hallmark feature of sickle cell disease (SCD). Recurrent and unpredictable acute pain due to vaso-oclussive crises (VOC) is unique to SCD; and can be superimposed on chronic pain. To examine the mechanisms underlying pain in SCD, we performed RNA sequencing of dorsal root ganglion (DRG) of transgenic sickle mice and their age-matched control mice expressing normal human hemoglobin A, at 2 and 5 months of age. Sickle and control mice of both ages were equally divided into hypoxia/reoxygenation (to simulate VOC) and normoxia treatment, resulting in eight groups of mice. Each group had at least six mice. RNA isolated from the DRG was sequenced and paired-end 50 bp sequencing data were generated using Illumina's HiSeq 2000. This large dataset can serve as a resource for examining transcriptional changes in the DRG that are associated with age and hypoxia/reoxygenation associated signatures of nociceptive mechanisms underlying chronic and acute pain, respectively.
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Affiliation(s)
- Jinny A. Paul
- Vascular Biology Center, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Anupam Aich
- Vascular Biology Center, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Juan E. Abrahante
- University of Minnesota Informatics Institute, Minneapolis, Minnesota 55455, USA
| | - Ying Wang
- Vascular Biology Center, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Rebecca S. LaRue
- Minnesota Super Computing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Susan K. Rathe
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Krystina Kalland
- Vascular Biology Center, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Aditya Mittal
- Vascular Biology Center, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Ritu Jha
- Vascular Biology Center, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Fei Peng
- Vascular Biology Center, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - David A. Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Pediatrics, Division of Hematology, Oncology and Transplantations, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Anindya Bagchi
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Urology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Kalpna Gupta
- Vascular Biology Center, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Reed KM, Mendoza KM, Abrahante JE, Barnes NE, Velleman SG, Strasburg GM. Response of turkey muscle satellite cells to thermal challenge. I. transcriptome effects in proliferating cells. BMC Genomics 2017; 18:352. [PMID: 28477619 PMCID: PMC5420122 DOI: 10.1186/s12864-017-3740-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 01/23/2017] [Accepted: 04/27/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Climate change poses a multi-dimensional threat to food and agricultural systems as a result of increased risk to animal growth, development, health, and food product quality. This study was designed to characterize transcriptional changes induced in turkey muscle satellite cells cultured under cold or hot thermal challenge to better define molecular mechanisms by which thermal stress alters breast muscle ultrastructure. RESULTS Satellite cells isolated from the pectoralis major muscle of 7-weeks-old male turkeys from two breeding lines (16 weeks body weight-selected and it's randombred control) were proliferated in culture at 33 °C, 38 °C or 43 °C for 72 h. Total RNA was isolated and 12 libraries subjected to RNAseq analysis. Statistically significant differences in gene expression were observed among treatments and between turkey lines with a greater number of genes altered by cold treatment than by hot and fewer differences observed between lines than between temperatures. Pathway analysis found that cold treatment resulted in an overrepresentation of genes involved in cell signaling/signal transduction and cell communication/cell signaling as compared to control (38 °C). Heat-treated muscle satellite cells showed greater tendency towards expression of genes related to muscle system development and differentiation. CONCLUSIONS This study demonstrates significant transcriptome effects on turkey skeletal muscle satellite cells exposed to thermal challenge. Additional effects on gene expression could be attributed to genetic selection for 16 weeks body weight (muscle mass). New targets are identified for further research on the differential control of satellite cell proliferation in poultry.
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Affiliation(s)
- Kent M. Reed
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN USA
| | - Kristelle M. Mendoza
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN USA
| | - Juan E. Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN USA
| | - Natalie E. Barnes
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN USA
| | - Sandra G. Velleman
- Department of Animal Sciences, The Ohio State University, Columbus, OH USA
- Ohio Agricultural Research and Development Center, Wooster, OH USA
| | - Gale M. Strasburg
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI USA
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Hill CM, Banga A, Abrahante JE, Yuan C, Mutch LA, Janecek J, O'Brien T, Graham ML, Dutton JR. Establishing a Large-Animal Model for In Vivo Reprogramming of Bile Duct Cells into Insulin-Secreting Cells to Treat Diabetes. HUM GENE THER CL DEV 2017; 28:87-95. [PMID: 28363269 DOI: 10.1089/humc.2017.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 12/12/2022] Open
Abstract
Type 1 diabetes manifests as autoimmune destruction of beta cells requiring metabolic management with an exogenous replacement of insulin, either by repeated injection of recombinant insulin or by transplantation of allogeneic islets from cadaveric donors. Both of these approaches have severe limitations. Repeated insulin injection requires intensive blood glucose monitoring, is expensive, and is associated with decreased quality-of-life measures. Islet transplantation, while highly effective, is severely limited by shortage of donor organs. Clinical translation of beta cells derived from pluripotent stem cells is also not yet a reality, and alternative approaches to solving the replacement of lost beta cell function are required. In vivo direct reprogramming offers an attractive approach to generating new endogenous insulin-secreting cells by permanently altering the phenotype of somatic cells after transient expression of transcription factors. Previously, we have successfully restored control of blood glucose in diabetic mice by reprogramming liver cells into glucose-sensitive insulin-secreting cells after the transient, simultaneous delivery of three transcription factors (Pdx1, Ngn3, and MafA) to the liver of diabetic mice, using an adenoviral vector (Ad-PNM). Establishing a clinically relevant, large-animal model is a critical next step in translating this approach beyond the proof-of-principle stage in rodents and allowing investigation of vector design, dose and delivery, host response to vector infusion, and establishment of suitable criteria for measuring safety and efficacy. In this feasibility study we infused Ad-PNM into the liver of three diabetic cynomolgus macaques via portal vein catheter. Vector presence and cargo gene and protein expression were detected in liver tissue after infusion with no adverse effects. Refinement of immune suppression significantly extended the period of exogenous PNM expression. This pilot study establishes the suitability of this large-animal model to examine the translation of this approach for treating diabetes.
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Affiliation(s)
- Caitlin M Hill
- 1 Stem Cell Institute, McGuire Translational Research Facility, University of Minnesota , Minneapolis, Minnesota
| | - Anannya Banga
- 1 Stem Cell Institute, McGuire Translational Research Facility, University of Minnesota , Minneapolis, Minnesota
| | - Juan E Abrahante
- 2 University of Minnesota Informatics Institute, University of Minnesota , Minneapolis, Minnesota
| | - Ce Yuan
- 1 Stem Cell Institute, McGuire Translational Research Facility, University of Minnesota , Minneapolis, Minnesota.,5 Bioinformatics and Computational Biology Program, University of Minnesota , Rochester, Minnesota
| | - Lucas A Mutch
- 3 Department of Surgery, Preclinical Research Center, University of Minnesota , Minneapolis, Minnesota
| | - Jody Janecek
- 3 Department of Surgery, Preclinical Research Center, University of Minnesota , Minneapolis, Minnesota
| | - Timothy O'Brien
- 1 Stem Cell Institute, McGuire Translational Research Facility, University of Minnesota , Minneapolis, Minnesota.,4 Department of Veterinary Population Medicine, University of Minnesota , St. Paul, Minnesota
| | - Melanie L Graham
- 3 Department of Surgery, Preclinical Research Center, University of Minnesota , Minneapolis, Minnesota.,4 Department of Veterinary Population Medicine, University of Minnesota , St. Paul, Minnesota
| | - James R Dutton
- 1 Stem Cell Institute, McGuire Translational Research Facility, University of Minnesota , Minneapolis, Minnesota
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Winterhoff BJ, Maile M, Mitra AK, Sebe A, Bazzaro M, Geller MA, Abrahante JE, Klein M, Hellweg R, Mullany SA, Beckman K, Daniel J, Starr TK. Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells. Gynecol Oncol 2017; 144:598-606. [PMID: 28111004 DOI: 10.1016/j.ygyno.2017.01.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 12/24/2022]
Abstract
OBJECTIVES The purpose of this study was to determine the level of heterogeneity in high grade serous ovarian cancer (HGSOC) by analyzing RNA expression in single epithelial and cancer associated stromal cells. In addition, we explored the possibility of identifying subgroups based on pathway activation and pre-defined signatures from cancer stem cells and chemo-resistant cells. METHODS A fresh, HGSOC tumor specimen derived from ovary was enzymatically digested and depleted of immune infiltrating cells. RNA sequencing was performed on 92 single cells and 66 of these single cell datasets passed quality control checks. Sequences were analyzed using multiple bioinformatics tools, including clustering, principle components analysis, and geneset enrichment analysis to identify subgroups and activated pathways. Immunohistochemistry for ovarian cancer, stem cell and stromal markers was performed on adjacent tumor sections. RESULTS Analysis of the gene expression patterns identified two major subsets of cells characterized by epithelial and stromal gene expression patterns. The epithelial group was characterized by proliferative genes including genes associated with oxidative phosphorylation and MYC activity, while the stromal group was characterized by increased expression of extracellular matrix (ECM) genes and genes associated with epithelial-to-mesenchymal transition (EMT). Neither group expressed a signature correlating with published chemo-resistant gene signatures, but many cells, predominantly in the stromal subgroup, expressed markers associated with cancer stem cells. CONCLUSIONS Single cell sequencing provides a means of identifying subpopulations of cancer cells within a single patient. Single cell sequence analysis may prove to be critical for understanding the etiology, progression and drug resistance in ovarian cancer.
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Affiliation(s)
- Boris J Winterhoff
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Makayla Maile
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Amit Kumar Mitra
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN, USA
| | - Attila Sebe
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Martina Bazzaro
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Melissa A Geller
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, USA
| | - Molly Klein
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Raffaele Hellweg
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA
| | - Sally A Mullany
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA
| | - Kenneth Beckman
- Genomics Center, University of Minnesota, Minneapolis, MN, USA
| | - Jerry Daniel
- Genomics Center, University of Minnesota, Minneapolis, MN, USA
| | - Timothy K Starr
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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Gazestani VH, Hampton M, Abrahante JE, Salavati R, Zimmer SL. circTAIL-seq, a targeted method for deep analysis of RNA 3' tails, reveals transcript-specific differences by multiple metrics. RNA 2016; 22:477-86. [PMID: 26759453 PMCID: PMC4748824 DOI: 10.1261/rna.054494.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/09/2015] [Indexed: 05/28/2023]
Abstract
Post-transcriptionally added RNA 3' nucleotide extensions, or tails, impose numerous regulatory effects on RNAs, including effects on RNA turnover and translation. However, efficient methods for in-depth tail profiling of a transcript of interest are still lacking, hindering available knowledge particularly of tail populations that are highly heterogeneous. Here, we developed a targeted approach, termed circTAIL-seq, to quantify both major and subtle differences of heterogeneous tail populations. As proof-of-principle, we show that circTAIL-seq quantifies the differences in tail qualities between two selected Trypanosoma brucei mitochondrial transcripts. The results demonstrate the power of the developed method in identification, discrimination, and quantification of different tail states that the population of one transcript can possess. We further show that circTAIL-seq can detect the tail characteristics for variants of transcripts that are not easily detectable by conventional approaches, such as degradation intermediates. Our findings are not only well supported by previous knowledge, but they also expand this knowledge and provide experimental evidence for previous hypotheses. In the future, this approach can be used to determine changes in tail qualities in response to environmental or internal stimuli, or upon silencing of genes of interest in mRNA-processing pathways. In summary, circTAIL-seq is an effective tool for comparing nonencoded RNA tails, especially when the tails are extremely variable or transcript of interest is low abundance.
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Affiliation(s)
- Vahid H Gazestani
- Institute of Parasitology, McGill University, Québec H9X 3V9, Canada
| | - Marshall Hampton
- Department of Mathematics, University of Minnesota Duluth, Duluth, Minnesota 55812, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Reza Salavati
- Institute of Parasitology, McGill University, Québec H9X 3V9, Canada
| | - Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, Minnesota 55812, USA
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Been RA, Linden MA, Hager CJ, DeCoursin KJ, Abrahante JE, Landman SR, Steinbach M, Sarver AL, Largaespada DA, Starr TK. Genetic signature of histiocytic sarcoma revealed by a sleeping beauty transposon genetic screen in mice. PLoS One 2014; 9:e97280. [PMID: 24827933 PMCID: PMC4020815 DOI: 10.1371/journal.pone.0097280] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 04/18/2014] [Indexed: 02/06/2023] Open
Abstract
Histiocytic sarcoma is a rare, aggressive neoplasm that responds poorly to therapy. Histiocytic sarcoma is thought to arise from macrophage precursor cells via genetic changes that are largely undefined. To improve our understanding of the etiology of histiocytic sarcoma we conducted a forward genetic screen in mice using the Sleeping Beauty transposon as a mutagen to identify genetic drivers of histiocytic sarcoma. Sleeping Beauty mutagenesis was targeted to myeloid lineage cells using the Lysozyme2 promoter. Mice with activated Sleeping Beauty mutagenesis had significantly shortened lifespan and the majority of these mice developed tumors resembling human histiocytic sarcoma. Analysis of transposon insertions identified 27 common insertion sites containing 28 candidate cancer genes. Several of these genes are known drivers of hematological neoplasms, like Raf1, Fli1, and Mitf, while others are well-known cancer genes, including Nf1, Myc, Jak2, and Pten. Importantly, several new potential drivers of histiocytic sarcoma were identified and could serve as targets for therapy for histiocytic sarcoma patients.
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Affiliation(s)
- Raha A. Been
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Comparative and Molecular Biosciences, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Michael A. Linden
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Courtney J. Hager
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Krista J. DeCoursin
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Juan E. Abrahante
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Sean R. Landman
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Michael Steinbach
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Aaron L. Sarver
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - David A. Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Timothy K. Starr
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
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Robinson SR, Abrahante JE, Johnson CR, Murtaugh MP. Purifying selection in porcine reproductive and respiratory syndrome virus ORF5a protein influences variation in envelope glycoprotein 5 glycosylation. Infect Genet Evol 2013; 20:362-8. [PMID: 24084290 DOI: 10.1016/j.meegid.2013.09.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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: 03/15/2013] [Revised: 09/05/2013] [Accepted: 09/21/2013] [Indexed: 02/06/2023]
Abstract
Porcine reproductive and respiratory syndrome virus ORF5a protein is encoded in an alternate open reading frame upstream of the major envelope glycoprotein (GP5) in subgenomic mRNA5. Bioinformatic analysis of 3466 type 2 PRRSV sequences showed that the two proteins have co-evolved through a fine balance of purifying codon usage to maintain a conserved RQ-rich motif in ORF5a protein, while eliciting a variable N-linked glycosylation motif in the alternative GP5 reading frame. Conservation of the ORF5a protein RQ-motif also explains an anomalous uracil desert in GP5 hypervariable glycosylation region. The N-terminus of the mature GP5 protein was confirmed to start with amino acid 32, the hypervariable region of the ectodomain. Since GP5 glycosylation variability is assumed to result from immunological selection against neutralizing antibodies, these findings show that an alternative possibility unrelated to immunological selection not only exists, but provides a foundation for investigating previously unsuspected aspects of PRRSV biology. Understanding functional consequences of subtle nucleotide sequence modifications in the region responsible for critical function in ORF5a protein and GP5 glycosylation is essential for rational design of new vaccines against PRRS.
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Affiliation(s)
- Sally R Robinson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA.
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41
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Johnson TJ, Abrahante JE, Hunter SS, Hauglund M, Tatum FM, Maheswaran SK, Briggs RE. Comparative genome analysis of an avirulent and two virulent strains of avian Pasteurella multocida reveals candidate genes involved in fitness and pathogenicity. BMC Microbiol 2013; 13:106. [PMID: 23672515 PMCID: PMC3660278 DOI: 10.1186/1471-2180-13-106] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [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: 01/02/2013] [Accepted: 05/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pasteurella multocida is the etiologic agent of fowl cholera, a highly contagious and severe disease of poultry causing significant mortality and morbidity throughout the world. All types of poultry are susceptible to fowl cholera. Turkeys are most susceptible to the peracute/acute forms of the disease while chickens are most susceptible to the acute and chronic forms of the disease. The whole genome of the Pm70 strain of P. multocida was sequenced and annotated in 2001. The Pm70 strain is not virulent to chickens and turkeys. In contrast, strains X73 and P1059 are highly virulent to turkeys, chickens, and other poultry species. In this study, we sequenced the genomes of P. multocida strains X73 and P1059 and undertook a detailed comparative genome analysis with the avirulent Pm70 strain. The goal of this study was to identify candidate genes in the virulent strains that may be involved in pathogenicity of fowl cholera disease. RESULTS Comparison of virulent versus avirulent avian P. multocida genomes revealed 336 unique genes among the P1059 and/or X73 genomes compared to strain Pm70. Genes of interest within this subset included those encoding an L-fucose transport and utilization system, several novel sugar transport systems, and several novel hemagglutinins including one designated PfhB4. Additionally, substantial amino acid variation was observed in many core outer membrane proteins and single nucleotide polymorphism analysis confirmed a higher dN/dS ratio within proteins localized to the outer membrane. CONCLUSIONS Comparative analyses of highly virulent versus avirulent avian P. multocida identified a number of genomic differences that may shed light on the ability of highly virulent strains to cause disease in the avian host, including those that could be associated with enhanced virulence or fitness.
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Affiliation(s)
- Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St, Paul, MN, USA.
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Robinson SR, Figueiredo MC, Abrahante JE, Murtaugh MP. Immune response to ORF5a protein immunization is not protective against porcine reproductive and respiratory syndrome virus infection. Vet Microbiol 2013; 164:281-5. [PMID: 23578707 DOI: 10.1016/j.vetmic.2013.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/26/2013] [Accepted: 03/01/2013] [Indexed: 10/27/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is an enveloped RNA virus responsible for PRRS in swine, a disease with globally significant animal welfare and economic concerns. There is no specific treatment and variably effective immune protection. Molecular mechanisms responsible for virulence, pathogenesis and protective immune response remain poorly understood. These factors limit progress toward development of effective measures for prevention and treatment of PRRS. A novel PRRSV ORF5a protein, encoded in an open reading frame (ORF) that overlaps the major envelope glycoprotein GP5 ORF, was recently identified. Because ORF5a is highly conserved in diverse PRRSV isolates, is a structural protein in the virion, and elicits a specific antibody response in infected pigs, we investigated its potential role in immune protection against PRRSV infection. Pigs immunized with ORF5a protein had robust serologic responses. However, the antibodies did not neutralize virus, and immunity did not protect against challenge infection. We conclude from these findings that the ORF5a antibody response is neither neutralizing nor protective.
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Affiliation(s)
- Sally R Robinson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA.
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Abrahante JE, Johnson TJ, Hunter SS, Maheswaran SK, Hauglund MJ, Bayles DO, Tatum FM, Briggs RE. Draft Genome Sequences of Two Virulent Serotypes of Avian Pasteurella multocida. Genome Announc 2013; 1:e00058-12. [PMID: 23405337 PMCID: PMC3569333 DOI: 10.1128/genomea.00058-12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 11/19/2012] [Indexed: 11/20/2022]
Abstract
Here we report the draft genome sequences of two virulent avian strains of Pasteurella multocida. Comparative analyses of these genomes were done with the published genome sequence of avirulent P. multocida strain Pm70.
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Affiliation(s)
- Juan E. Abrahante
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, USA
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, USA
| | - Samuel S. Hunter
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Samuel K. Maheswaran
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, USA
| | - Melissa J. Hauglund
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, Iowa, USA
| | - Darrell O. Bayles
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, Iowa, USA
| | - Fred M. Tatum
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, Iowa, USA
| | - Robert E. Briggs
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, Iowa, USA
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Abrahante JE, Zhang JW, Rossow K, Zimmerman JJ, Murtaugh MP. Surveillance of Bungowannah pestivirus in the upper Midwestern USA. Transbound Emerg Dis 2012; 61:375-7. [PMID: 23343245 DOI: 10.1111/tbed.12035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [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: 08/11/2012] [Indexed: 02/05/2023]
Abstract
Pestiviruses, a genetically and antigenically highly diverse group, include one of the most historically significant swine pathogens, that is, classical swine fever virus. In Australia, investigations into swine outbreaks characterized by neonatal mortality, stillbirths and mummified foetuses resulted in the discovery of a new pestivirus, Bungowannah virus. This finding raised the possibility that Bungowannah virus, or a variant thereof, was circulating in swine herds elsewhere in the World. If so, it raised the possibility of a pestivirus emerging as a new swine disease with unknown consequences for animal health and food safety. Thus, we developed three specific qRT-PCR assays to evaluate tissue samples from undiagnosed cases of abortion or respiratory disease for evidence of Bungowannah virus. Examination of 64 samples collected between the Fall of 2007 and Spring of 2010 tested negative for all three genes examined. We conclude that Bungowannah-like pestivirus is unlikely to be present in swine in the upper Midwestern USA.
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Affiliation(s)
- J E Abrahante
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA
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Gnanandarajah JS, Johnson TJ, Kim HB, Abrahante JE, Lulich JP, Murtaugh MP. Comparative faecal microbiota of dogs with and without calcium oxalate stones. J Appl Microbiol 2012; 113:745-56. [PMID: 22788835 DOI: 10.1111/j.1365-2672.2012.05390.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 07/03/2012] [Accepted: 07/04/2012] [Indexed: 12/13/2022]
Abstract
AIMS The absence of enteric oxalate-metabolizing bacterial species (OMBS) increases the likelihood of calcium oxalate (CaOx) urolithiasis in humans and dogs. The goal of this study was to compare the gut microbiota of healthy dogs and CaOx stone formed dogs (CaOx-dogs), especially with respect to OMBS. METHODS AND RESULTS Faecal samples from healthy and CaOx-dogs were obtained to analyse the hindgut microbiota by sequencing the V3 region of bacterial 16S rDNA. In total, 1223 operational taxonomic units (OTUs) were identified at 97% identity. Only 38% of these OTUs were shared by both groups. Significant differences in the relative abundance of 152 OTUs and 36 genera were observed between the two groups of dogs. CONCLUSIONS The faecal microbiota of healthy dogs is distinct from that of CaOx-dogs, indicating that the microbiota is altered in CaOx-dogs. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study that has compared the gut microbial diversity in healthy and CaOx-dogs. Results of this study indicate the future need for functional and comparative analyses of the total array of oxalate-metabolizing genes between healthy and CaOx stone formers, rather than focusing on specific bacterial species, to understand the critical role of OMBS in CaOx urolithiasis.
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Affiliation(s)
- J S Gnanandarajah
- Departments of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA
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Abrahante JE, Martins K, Papas KK, Hering BJ, Schuurman HJ, Murtaugh MP. Microbiological safety of porcine islets: comparison with source pig. Xenotransplantation 2011; 18:88-93. [PMID: 21496116 DOI: 10.1111/j.1399-3089.2011.00632.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Pig islet donors intended for clinical xenotransplantation for the treatment of diabetes must meet stringent conditions. Among others, viruses with the potential to cross the species barrier should be excluded from the herd: this list includes encephalomyocarditis virus (EMCV), hepatitis E virus (HEV), porcine cytomegalovirus (PCMV) and porcine γ-lymphotropic herpesvirus (PLHV). As an islet product is isolated from the pancreas and then subjected to culture before implantation, the question is raised whether islets could be negative even if the animal itself is positive for a distinct pathogen. METHODS To answer this question, sensitive quantitative real-time PCR assays were established for EMCV, HEV, PCMV and PLHV. Twelve adult animals from a high-hygienic herd were then evaluated; testing tissues, where the virus is expected to reside in latent infection, testing islets immediately after isolation, and then isolated islets after a 7-day culture. RESULTS None of the tissues tested positive for EMCV, HEV or PLHV. PCMV was observed in spleen tissue from six animals: three of these six animals were positive for isolated islets, and two of these three cases were also positive for islets after culture. Older animals in particular showed positivity, and within a given litter not all animals were PCMV positive. CONCLUSIONS These data fit with spread through the herd by horizontal transmission, not in utero infection. PCMV has to be excluded from the herd to ensure that islets for transplantation are negative for PCMV.
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Affiliation(s)
- Juan E Abrahante
- Department of Veterinary & Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA
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Murtaugh MP, Stadejek T, Abrahante JE, Lam TTY, Leung FCC. The ever-expanding diversity of porcine reproductive and respiratory syndrome virus. Virus Res 2010; 154:18-30. [PMID: 20801173 DOI: 10.1016/j.virusres.2010.08.015] [Citation(s) in RCA: 229] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 08/10/2010] [Accepted: 08/16/2010] [Indexed: 02/06/2023]
Abstract
Porcine reproductive and respiratory syndrome (PRRS) virus appeared 20 years ago as the cause of a new disease in swine. Today PRRS is the most significant swine disease worldwide in spite of intensive immunological interventions. The virus showed remarkable genetic variation with two geographically distinct genotypes at the time of its discovery, indicating the possibility of prolonged evolutionary divergence prior to its appearance as a swine pathogen. Since then, both type 1 and type 2 have spread geographically, radiated genetically, and acquired new phenotypic characteristics, especially increased virulence. Here, we explore various hypotheses that might account for rapid expansion and diversification of PRRSV, including mechanisms specific to PRRSV and other arteriviruses, cellular modification processes, and immunological selection. Phylogenetic analysis of PRRSV has provided a broadly applicable means to relate diverse isolates, but it does not explain biological variation in virulence or immunological cross-protection. We present other methods of classification and review their limitations. Major questions about PRRSV remain unanswered despite intensive investigation, suggesting that the interaction of PRRSV with pigs involves novel biological processes that may be relevant to other RNA virus and host interactions.
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Affiliation(s)
- Michael P Murtaugh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA.
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de Abin MF, Spronk G, Wagner M, Fitzsimmons M, Abrahante JE, Murtaugh MP. Comparative infection efficiency of Porcine reproductive and respiratory syndrome virus field isolates on MA104 cells and porcine alveolar macrophages. Can J Vet Res 2009; 73:200-204. [PMID: 19794892 PMCID: PMC2705074] [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] [Subscribe] [Scholar Register] [Received: 02/10/2008] [Accepted: 06/19/2008] [Indexed: 05/28/2023]
Abstract
Isolation of Porcine reproductive and respiratory syndrome virus (PRRSV) on MA104 or MARC-145 cells is frequently used in PRRS diagnosis. However, the ability of recent field isolates to grow on these established simian cell lines has not been determined. The aim of this study was to characterize the growth of PRRSV field isolates on primary porcine alveolar macrophages (PAMs) and MA104 cells in comparison with the growth of the laboratory-adapted strain VR-2332. A cytopathic effect was observed in 70% of serum samples after 1 passage on PAMs and was verified by immunofluorescent staining or reverse transcriptase-polymerase chain reaction. Field isolate growth was observed on MA104 cells for only 1 of 50 serum samples after 14 d. Strain VR-2332 grew readily in MA104 cells [maximum titer, 10(7) TCID(50) (median tissue culture infective dose) per milliliter at 30 h] but not in PAMs (10(2) TCID(50)/mL at 72 h). These results show that PAMs are superior to simian cells for diagnostic isolation of current field PRRSV strains.
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Affiliation(s)
| | | | | | | | | | - Michael P. Murtaugh
- Address all correspondence to Dr. Michael P. Murtaugh; telephone: (612) 625-6735; fax: (612) 625-5203; e-mail:
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Jenkins MC, Higgins J, Abrahante JE, Kniel KE, O'Brien C, Trout J, Lancto CA, Abrahamsen MS, Fayer R. Fecundity of Cryptosporidium parvum is correlated with intracellular levels of the viral symbiont CPV. Int J Parasitol 2007; 38:1051-5. [PMID: 18096164 DOI: 10.1016/j.ijpara.2007.11.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 11/09/2007] [Accepted: 11/13/2007] [Indexed: 10/22/2022]
Abstract
Differences in the virulence and fecundity of Cryptosporidium parvum isolates have been observed by several researchers studying cryptosporidiosis. The purpose of the present study was to determine if there was a correlation between intracellular levels of the viral symbiont CPV in C. parvum and fecundity of two isolates of the parasite, namely C. parvum Beltsville (B) and C. parvum Iowa (I). Dairy calves infected with 10(6)C. parvum-B excreted 5-fold more oocysts compared with calves infected with the same number of C. parvum-I oocysts. The increased fecundity of the former strain was corroborated by semi-quantitative PCR assay of DNA isolated from cell cultures infected with either C. parvum-B or C. parvum-I. Quantitative reverse transcriptase-PCR analysis of viral RNA revealed a 3-fold greater number of CPV in C. parvum-B compared with C. parvum-I oocysts. These findings may indicate a role for CPV in fecundity and possibly virulence of C. parvum.
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Affiliation(s)
- M C Jenkins
- Animal Parasitic Diseases Laboratory, ARS, USDA, Beltsville, MD, USA.
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50
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Templeton TJ, Iyer LM, Anantharaman V, Enomoto S, Abrahante JE, Subramanian GM, Hoffman SL, Abrahamsen MS, Aravind L. Comparative analysis of apicomplexa and genomic diversity in eukaryotes. Genome Res 2004; 14:1686-95. [PMID: 15342554 PMCID: PMC515313 DOI: 10.1101/gr.2615304] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2004] [Accepted: 06/14/2004] [Indexed: 11/24/2022]
Abstract
The apicomplexans Plasmodium and Cryptosporidium have developed distinctive adaptations via lineage-specific gene loss and gene innovation in the process of diverging from a common parasitic ancestor. The two lineages have acquired distinct but overlapping sets of surface protein adhesion domains typical of animal proteins, but in no case do they share multidomain architectures identical to animals. Cryptosporidium, but not Plasmodium, possesses an animal-type O-linked glycosylation pathway, along with >30 predicted surface proteins having mucin-like segments. The two parasites have notable qualitative differences in conserved protein architectures associated with chromatin dynamics and transcription. Cryptosporidium shows considerable reduction in the number of introns and a concomitant loss of spliceosomal machinery components. We also describe additional molecular characteristics distinguishing Apicomplexa from other eukaryotes for which complete genome sequences are available.
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Affiliation(s)
- Thomas J Templeton
- Department of Microbiology and Immunology, Weill Medical College and the Program in Immunology and Microbial Pathogenesis, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, USA.
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