1
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Murray G, Bais P, Hatton C, Tadenev ALD, Hoffmann BR, Stodola TJ, Morelli KH, Pratt SL, Schroeder D, Doty R, Fiehn O, John SWM, Bult CJ, Cox GA, Burgess RW. Mouse models of NADK2 deficiency analyzed for metabolic and gene expression changes to elucidate pathophysiology. Hum Mol Genet 2022; 31:4055-4074. [PMID: 35796562 DOI: 10.1093/hmg/ddac151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
NADK2 encodes the mitochondrial form of NAD Kinase, which phosphorylates nicotinamide adenine dinucleotide (NAD). Rare recessive mutations in human NADK2 are associated with a syndromic neurological mitochondrial disease that includes metabolic changes such as hyperlysinemia and 2,4 dienoyl CoA reductase (DECR) deficiency. However, the full pathophysiology resulting from NADK2 deficiency is not known. Here we describe two chemically-induced mouse mutations in Nadk2, S326L and S330P, which cause a severe neuromuscular disease and shorten lifespan. The S330P allele was characterized in detail and shown to have marked denervation of neuromuscular junctions by 5 weeks of age and muscle atrophy by 11 weeks of age. Cerebellar Purkinje cells also showed progressive degeneration in this model. Transcriptome profiling on brain and muscle was performed at early and late disease stages. In addition, metabolomic profiling was performed on brain, muscle, liver, and spinal cord at the same ages, and plasma at 5 weeks. Combined transcriptomic and metabolomic analyses identified hyperlysinemia, DECR deficiency, and generalized metabolic dysfunction in Nadk2 mutant mice, indicating relevance to the human disease. We compared findings from the Nadk model to equivalent RNAseq and metabolomic datasets from a mouse model of infantile neuroaxonal dystrophy, caused by recessive mutations in Pla2g6. This enabled us to identify disrupted biological processes that are common between these mouse models of neurological disease, as well as those processes that are gene-specific. These findings improve our understanding of the pathophysiology of neuromuscular diseases, and describe mouse models that will be useful for future preclinical studies.
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Affiliation(s)
- G Murray
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA.,The Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469USA
| | - P Bais
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA
| | - C Hatton
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA
| | - A L D Tadenev
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA
| | - B R Hoffmann
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA
| | - T J Stodola
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA
| | - K H Morelli
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA.,The Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469USA
| | - S L Pratt
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA.,Neuroscience Program, Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - D Schroeder
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA
| | - R Doty
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA
| | - O Fiehn
- West Coast Metabolomics Center, University of California Davis, 451 Health Science Dr., Davis, CA, 95618USA
| | - S W M John
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA.,Howard Hughes Medical Institute.,Department of Ophthalmology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032USA
| | - C J Bult
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA.,The Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469USA
| | - G A Cox
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA.,The Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469USA.,Neuroscience Program, Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - R W Burgess
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609USA.,The Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469USA.,Neuroscience Program, Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
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2
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Peek SL, Bosch PJ, Bahl E, Iverson BJ, Parida M, Bais P, Manak JR, Michaelson JJ, Burgess RW, Weiner JA. p53-mediated neurodegeneration in the absence of the nuclear protein Akirin2. iScience 2022; 25:103814. [PMID: 35198879 PMCID: PMC8844820 DOI: 10.1016/j.isci.2022.103814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/04/2022] [Accepted: 01/20/2022] [Indexed: 12/13/2022] Open
Abstract
Proper gene regulation is critical for both neuronal development and maintenance as the brain matures. We previously demonstrated that Akirin2, an essential nuclear protein that interacts with transcription factors and chromatin remodeling complexes, is required for the embryonic formation of the cerebral cortex. Here we show that Akirin2 plays a mechanistically distinct role in maintaining healthy neurons during cortical maturation. Restricting Akirin2 loss to excitatory cortical neurons resulted in progressive neurodegeneration via necroptosis and severe cortical atrophy with age. Comparing transcriptomes from Akirin2-null postnatal neurons and cortical progenitors revealed that targets of the tumor suppressor p53, a regulator of both proliferation and cell death encoded by Trp53, were consistently upregulated. Reduction of Trp53 rescued neurodegeneration in Akirin2-null neurons. These data: (1) implicate Akirin2 as a critical neuronal maintenance protein, (2) identify p53 pathways as mediators of Akirin2 functions, and (3) suggest Akirin2 dysfunction may be relevant to neurodegenerative diseases.
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Affiliation(s)
- Stacey L Peek
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242, USA.,Department of Biology, University of Iowa, Iowa City, IA 52242, USA.,Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Peter J Bosch
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.,Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Ethan Bahl
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA.,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA.,Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Brianna J Iverson
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.,Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Mrutyunjaya Parida
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.,Departments of Pediatrics, University of Iowa, Iowa City, IA 52242, USA.,Roy J. Carver Center for Genomics, University of Iowa, Iowa City, IA 52242, USA
| | - Preeti Bais
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - J Robert Manak
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.,Departments of Pediatrics, University of Iowa, Iowa City, IA 52242, USA.,Roy J. Carver Center for Genomics, University of Iowa, Iowa City, IA 52242, USA
| | - Jacob J Michaelson
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA.,Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.,Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA 52242, USA.,Department of Communication Sciences and Disorders, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA 52242, USA.,Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA 52242, USA
| | | | - Joshua A Weiner
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.,Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA.,Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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3
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Liu KH, Lee CM, Singer G, Bais P, Castellanos F, Woodworth MH, Ziegler TR, Kraft CS, Miller GW, Li S, Go YM, Morgan ET, Jones DP. Large scale enzyme based xenobiotic identification for exposomics. Nat Commun 2021; 12:5418. [PMID: 34521839 PMCID: PMC8440538 DOI: 10.1038/s41467-021-25698-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
Advances in genomics have revealed many of the genetic underpinnings of human disease, but exposomics methods are currently inadequate to obtain a similar level of understanding of environmental contributions to human disease. Exposomics methods are limited by low abundance of xenobiotic metabolites and lack of authentic standards, which precludes identification using solely mass spectrometry-based criteria. Here, we develop and validate a method for enzymatic generation of xenobiotic metabolites for use with high-resolution mass spectrometry (HRMS) for chemical identification. Generated xenobiotic metabolites were used to confirm identities of respective metabolites in mice and human samples based upon accurate mass, retention time and co-occurrence with related xenobiotic metabolites. The results establish a generally applicable enzyme-based identification (EBI) for mass spectrometry identification of xenobiotic metabolites and could complement existing criteria for chemical identification.
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Affiliation(s)
- Ken H. Liu
- grid.189967.80000 0001 0941 6502Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia USA
| | - Choon M. Lee
- grid.189967.80000 0001 0941 6502Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia USA
| | - Grant Singer
- grid.189967.80000 0001 0941 6502Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia USA
| | - Preeti Bais
- The Jackson Laboratory for Genomic Medicine, Atlanta, Connecticut USA
| | | | - Michael H. Woodworth
- grid.189967.80000 0001 0941 6502Division of Infectious Disease, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia USA
| | - Thomas R. Ziegler
- grid.189967.80000 0001 0941 6502Division of Endocrinology, Metabolism and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia USA
| | - Colleen S. Kraft
- grid.189967.80000 0001 0941 6502Division of Infectious Disease, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia USA ,grid.189967.80000 0001 0941 6502Emory University School of Medicine, Department of Pathology and Laboratory Medicine, Atlanta, Georgia USA
| | - Gary W. Miller
- grid.21729.3f0000000419368729Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York USA
| | - Shuzhao Li
- The Jackson Laboratory for Genomic Medicine, Atlanta, Connecticut USA
| | - Young-Mi Go
- grid.189967.80000 0001 0941 6502Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia USA
| | - Edward T. Morgan
- grid.189967.80000 0001 0941 6502Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia USA
| | - Dean P. Jones
- grid.189967.80000 0001 0941 6502Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia USA
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4
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Spaulding EL, Hines TJ, Bais P, Tadenev ALD, Schneider R, Jewett D, Pattavina B, Pratt SL, Morelli KH, Stum MG, Hill DP, Gobet C, Pipis M, Reilly MM, Jennings MJ, Horvath R, Bai Y, Shy ME, Alvarez-Castelao B, Schuman EM, Bogdanik LP, Storkebaum E, Burgess RW. The integrated stress response contributes to tRNA synthetase-associated peripheral neuropathy. Science 2021; 373:1156-1161. [PMID: 34516839 PMCID: PMC8908546 DOI: 10.1126/science.abb3414] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [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] [Indexed: 02/02/2023]
Abstract
Dominant mutations in ubiquitously expressed transfer RNA (tRNA) synthetase genes cause axonal peripheral neuropathy, accounting for at least six forms of Charcot-Marie-Tooth (CMT) disease. Genetic evidence in mouse and Drosophila models suggests a gain-of-function mechanism. In this study, we used in vivo, cell type–specific transcriptional and translational profiling to show that mutant tRNA synthetases activate the integrated stress response (ISR) through the sensor kinase GCN2 (general control nonderepressible 2). The chronic activation of the ISR contributed to the pathophysiology, and genetic deletion or pharmacological inhibition of Gcn2 alleviated the peripheral neuropathy. The activation of GCN2 suggests that the aberrant activity of the mutant tRNA synthetases is still related to translation and that inhibiting GCN2 or the ISR may represent a therapeutic strategy in CMT.
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Affiliation(s)
- E. L. Spaulding
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
| | - T. J. Hines
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - P. Bais
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - A. L. D. Tadenev
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - R. Schneider
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - D. Jewett
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - B. Pattavina
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - S. L. Pratt
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- Neuroscience Program, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, 02111 USA
| | - K. H. Morelli
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
| | - M. G. Stum
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - D. P. Hill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - C. Gobet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - M. Pipis
- MRC Centre for Neuromuscular Diseases, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - M. M. Reilly
- MRC Centre for Neuromuscular Diseases, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - M. J. Jennings
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - R. Horvath
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Y. Bai
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - M. E. Shy
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | | | - E. M. Schuman
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - L. P. Bogdanik
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - E. Storkebaum
- Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - R. W. Burgess
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
- Neuroscience Program, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, 02111 USA
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5
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Garrett AM, Bosch PJ, Steffen DM, Fuller LC, Marcucci CG, Koch AA, Bais P, Weiner JA, Burgess RW. CRISPR/Cas9 interrogation of the mouse Pcdhg gene cluster reveals a crucial isoform-specific role for Pcdhgc4. PLoS Genet 2019; 15:e1008554. [PMID: 31877124 PMCID: PMC6957209 DOI: 10.1371/journal.pgen.1008554] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/13/2020] [Accepted: 12/05/2019] [Indexed: 12/18/2022] Open
Abstract
The mammalian Pcdhg gene cluster encodes a family of 22 cell adhesion molecules, the gamma-Protocadherins (γ-Pcdhs), critical for neuronal survival and neural circuit formation. The extent to which isoform diversity–a γ-Pcdh hallmark–is required for their functions remains unclear. We used a CRISPR/Cas9 approach to reduce isoform diversity, targeting each Pcdhg variable exon with pooled sgRNAs to generate an allelic series of 26 mouse lines with 1 to 21 isoforms disrupted via discrete indels at guide sites and/or larger deletions/rearrangements. Analysis of 5 mutant lines indicates that postnatal viability and neuronal survival do not require isoform diversity. Surprisingly, given reports that it might not independently engage in trans-interactions, we find that γC4, encoded by Pcdhgc4, is the only critical isoform. Because the human orthologue is the only PCDHG gene constrained in humans, our results indicate a conserved γC4 function that likely involves distinct molecular mechanisms. The γ-Protocadherins (γ-Pcdhs) are a family of 22 molecules that serve many crucial functions during neural development. They can combine to form multimers at the cell surface, such that each combination specifically recognizes the same combination at the surface of other cells. In this way, 22 molecules can generate thousands of distinct recognition complexes. To test the extent to which molecular diversity is required for the γ-Pcdhs to serve their many functions, we used CRISPR/Cas9 gene editing to make a series of mouse mutants in which different combinations of the γ-Pcdhs are disrupted. We report 25 new mouse lines with between 1 and 21 intact members of the γ-Pcdh family. Further, we found that for the critical function of neuronal survival–and consequently the survival of the animal–the molecular diversity was not essential. Rather, a single member of the family called γC4 was the only one necessary or sufficient for this function; databases of human genome sequences suggest that this important role is conserved. These new strains will be invaluable for disentangling the role of molecular diversity in the γ-Pcdhs’ functions, and as we have already found, will help identify specific functions for specific γ-Pcdh family members.
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Affiliation(s)
- Andrew M. Garrett
- Department of Pharmacology and Department of Ophthalmology, Visual, and Anatomical Sciences, Wayne State University, Detroit, Michigan, United States of America
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- * E-mail: (AMG); (JAW); (RWB)
| | - Peter J. Bosch
- Department of Biology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - David M. Steffen
- Department of Biology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Leah C. Fuller
- Department of Biology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Charles G. Marcucci
- Department of Biology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Alexis A. Koch
- Department of Pharmacology and Department of Ophthalmology, Visual, and Anatomical Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Preeti Bais
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Joshua A. Weiner
- Department of Biology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail: (AMG); (JAW); (RWB)
| | - Robert W. Burgess
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- * E-mail: (AMG); (JAW); (RWB)
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6
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Chae YK, Anker JF, Oh MS, Bais P, Namburi S, Agte S, Giles FJ, Chuang JH. Mutations in DNA repair genes are associated with increased neoantigen burden and a distinct immunophenotype in lung squamous cell carcinoma. Sci Rep 2019; 9:3235. [PMID: 30824826 PMCID: PMC6397194 DOI: 10.1038/s41598-019-39594-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [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: 02/19/2018] [Accepted: 12/19/2018] [Indexed: 12/26/2022] Open
Abstract
Deficiencies in DNA repair pathways, including mismatch repair (MMR), have been linked to higher tumor mutation burden and improved response to immune checkpoint inhibitors. However, the significance of MMR mutations in lung cancer has not been well characterized, and the relevance of other processes, including homologous recombination (HR) and polymerase epsilon (POLE) activity, remains unclear. Here, we analyzed a dataset of lung squamous cell carcinoma samples from The Cancer Genome Atlas. Variants in DNA repair genes were associated with increased tumor mutation and neoantigen burden, which in turn were linked with greater tumor infiltration by activated T cells. The subset of tumors with DNA repair gene variants but without T cell infiltration exhibited upregulation of TGF-β and Wnt pathway genes, and a combined score incorporating these genes and DNA repair status accurately predicted immune cell infiltration. Finally, high neoantigen burden was positively associated with genes related to cytolytic activity and immune checkpoints. These findings provide evidence that DNA repair pathway defects and immunomodulatory genes together lead to specific immunophenotypes in lung squamous cell carcinoma and could potentially serve as biomarkers for immunotherapy.
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Affiliation(s)
- Young Kwang Chae
- Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA.
| | - Jonathan F Anker
- Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Michael S Oh
- Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Preeti Bais
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
| | - Sandeep Namburi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
| | - Sarita Agte
- Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Francis J Giles
- Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA.,Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT, 06032, USA
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7
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Wilmanns JC, Pandey R, Hon O, Chandran A, Schilling JM, Forte E, Wu Q, Cagnone G, Bais P, Philip V, Coleman D, Kocalis H, Archer SK, Pearson JT, Ramialison M, Heineke J, Patel HH, Rosenthal NA, Furtado MB, Costa MW. Metformin intervention prevents cardiac dysfunction in a murine model of adult congenital heart disease. Mol Metab 2019; 20:102-114. [PMID: 30482476 PMCID: PMC6358551 DOI: 10.1016/j.molmet.2018.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/06/2018] [Accepted: 11/10/2018] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE Congenital heart disease (CHD) is the most frequent birth defect worldwide. The number of adult patients with CHD, now referred to as ACHD, is increasing with improved surgical and treatment interventions. However the mechanisms whereby ACHD predisposes patients to heart dysfunction are still unclear. ACHD is strongly associated with metabolic syndrome, but how ACHD interacts with poor modern lifestyle choices and other comorbidities, such as hypertension, obesity, and diabetes, is mostly unknown. METHODS We used a newly characterized mouse genetic model of ACHD to investigate the consequences and the mechanisms associated with combined obesity and ACHD predisposition. Metformin intervention was used to further evaluate potential therapeutic amelioration of cardiac dysfunction in this model. RESULTS ACHD mice placed under metabolic stress (high fat diet) displayed decreased left ventricular ejection fraction. Comprehensive physiological, biochemical, and molecular analysis showed that ACHD hearts exhibited early changes in energy metabolism with increased glucose dependence as main cardiac energy source. These changes preceded cardiac dysfunction mediated by exposure to high fat diet and were associated with increased disease severity. Restoration of metabolic balance by metformin administration prevented the development of heart dysfunction in ACHD predisposed mice. CONCLUSIONS This study reveals that early metabolic impairment reinforces heart dysfunction in ACHD predisposed individuals and diet or pharmacological interventions can be used to modulate heart function and attenuate heart failure. Our study suggests that interactions between genetic and metabolic disturbances ultimately lead to the clinical presentation of heart failure in patients with ACHD. Early manipulation of energy metabolism may be an important avenue for intervention in ACHD patients to prevent or delay onset of heart failure and secondary comorbidities. These interactions raise the prospect for a translational reassessment of ACHD presentation in the clinic.
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Affiliation(s)
- Julia C Wilmanns
- Australian Regenerative Medicine Institute, Monash University, Australia; Department of Cardiology and Angiology, Experimental Cardiology, Hannover Medical School, Germany
| | | | | | - Anjana Chandran
- Australian Regenerative Medicine Institute, Monash University, Australia
| | - Jan M Schilling
- VA San Diego Healthcare System and Department of Anesthesiology, University of California San Diego, USA
| | | | - Qizhu Wu
- Monash Biomedical Imaging, Monash University, Australia
| | - Gael Cagnone
- Department of Pharmacology, Research Center of CHU Sainte-Justine, Canada
| | | | | | | | | | - Stuart K Archer
- Monash Bioinformatics Platform, Monash University, Australia; Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia
| | - James T Pearson
- Monash Biomedical Imaging, Monash University, Australia; Department of Physiology, Monash University, Australia; National Cerebral & Cardiovascular Center, Suita 565-8565, Japan
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, Australia; Systems Biology Institute, Australia
| | - Joerg Heineke
- Department of Cardiology and Angiology, Experimental Cardiology, Hannover Medical School, Germany
| | - Hemal H Patel
- VA San Diego Healthcare System and Department of Anesthesiology, University of California San Diego, USA
| | - Nadia A Rosenthal
- The Jackson Laboratory, USA; Australian Regenerative Medicine Institute, Monash University, Australia; National Heart and Lung Institute, Imperial College London, W12 0NN, UK
| | - Milena B Furtado
- The Jackson Laboratory, USA; Australian Regenerative Medicine Institute, Monash University, Australia
| | - Mauro W Costa
- The Jackson Laboratory, USA; Australian Regenerative Medicine Institute, Monash University, Australia.
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8
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Bais P, Namburi S, Gatti DM, Zhang X, Chuang JH. CloudNeo: a cloud pipeline for identifying patient-specific tumor neoantigens. Bioinformatics 2018; 33:3110-3112. [PMID: 28605406 PMCID: PMC5870764 DOI: 10.1093/bioinformatics/btx375] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 06/07/2017] [Indexed: 12/19/2022] Open
Abstract
Summary We present CloudNeo, a cloud-based computational workflow for identifying patient-specific tumor neoantigens from next generation sequencing data. Tumor-specific mutant peptides can be detected by the immune system through their interactions with the human leukocyte antigen complex, and neoantigen presence has recently been shown to correlate with anti T-cell immunity and efficacy of checkpoint inhibitor therapy. However computing capabilities to identify neoantigens from genomic sequencing data are a limiting factor for understanding their role. This challenge has grown as cancer datasets become increasingly abundant, making them cumbersome to store and analyze on local servers. Our cloud-based pipeline provides scalable computation capabilities for neoantigen identification while eliminating the need to invest in local infrastructure for data transfer, storage or compute. The pipeline is a Common Workflow Language (CWL) implementation of human leukocyte antigen (HLA) typing using Polysolver or HLAminer combined with custom scripts for mutant peptide identification and NetMHCpan for neoantigen prediction. We have demonstrated the efficacy of these pipelines on Amazon cloud instances through the Seven Bridges Genomics implementation of the NCI Cancer Genomics Cloud, which provides graphical interfaces for running and editing, infrastructure for workflow sharing and version tracking, and access to TCGA data. Availability and implementation The CWL implementation is at: https://github.com/TheJacksonLaboratory/CloudNeo. For users who have obtained licenses for all internal software, integrated versions in CWL and on the Seven Bridges Cancer Genomics Cloud platform (https://cgc.sbgenomics.com/, recommended version) can be obtained by contacting the authors. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Preeti Bais
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Sandeep Namburi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | - Xinyu Zhang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA.,Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06032, USA
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9
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Park LC, Rhee K, Kim WB, Cho A, Song J, Anker JF, Oh M, Bais P, Namburi S, Chuang J, Chae YK. Immunologic and clinical implications of CD73 expression in non-small cell lung cancer (NSCLC). J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.12050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Lee Chun Park
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Kyunghoon Rhee
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Won Bin Kim
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Anderson Cho
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Junho Song
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | | | - Michael Oh
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Preeti Bais
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | | | - Young Kwang Chae
- Northwestern Medicine Developmental Therapeutics Institute, Chicago, IL
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10
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Chae YK, Anker JF, Bais P, Namburi S, Giles FJ, Chuang JH. Mutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinoma. Oncotarget 2017; 9:7949-7960. [PMID: 29487705 PMCID: PMC5814272 DOI: 10.18632/oncotarget.23742] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/13/2017] [Indexed: 12/13/2022] Open
Abstract
Mutations in DNA repair genes lead to increased genomic instability and mutation frequency. These mutations represent potential biomarkers for cancer immunotherapy efficacy, as high tumor mutational burden has been associated with increased neo-antigens and tumor infiltrating lymphocytes. While mismatch repair mutations have successfully predicted response to anti-PD-1 therapy in colorectal and other cancers, they have not yet been tested for lung cancer, and few have investigated genes from other DNA repair pathways. We utilized TCGA samples to comprehensively immunophenotype lung tumors and analyze the links between DNA repair mutations, neo-antigen and total mutational burden, and tumor immune infiltration. Overall, 73% of lung tumors contained infiltration by at least one T cell subset, with high mutational burden tumors containing significantly increased infiltration by activated CD4 and CD8 T cells. Further, mutations in mismatch repair genes, homologous recombination genes, or POLE accurately predicted increased tumor mutational burden, neo-antigen load, and T cell infiltration. Finally, neo-antigen load correlated with expression of M1-polarized macrophage genes, PD-1, PD-L1, IFNγ, GZMB, and FASLG, among other immune-related genes. Overall, after defining the immune infiltrate in lung tumors, we demonstrate the potential value of utilizing gene mutations from multiple DNA repair pathways as biomarkers for lung cancer immunotherapy.
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Affiliation(s)
- Young Kwang Chae
- Northwestern University Feinberg School of Medicine, Chicago, 60611, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, 60611, IL, USA
| | - Jonathan F Anker
- Northwestern University Feinberg School of Medicine, Chicago, 60611, IL, USA
| | - Preeti Bais
- The Jackson Laboratory for Genomic Medicine, Farmington, 06030, CT, USA
| | - Sandeep Namburi
- The Jackson Laboratory for Genomic Medicine, Farmington, 06030, CT, USA
| | - Francis J Giles
- Northwestern University Feinberg School of Medicine, Chicago, 60611, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, 60611, IL, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, 06030, CT, USA.,Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, 06032, CT, USA
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11
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Bais P, Beebe K, Morelli KH, Currie ME, Norberg SN, Evsikov AV, Miers KE, Seburn KL, Guergueltcheva V, Kremensky I, Jordanova A, Bult CJ, Burgess RW. Metabolite profile of a mouse model of Charcot-Marie-Tooth type 2D neuropathy: implications for disease mechanisms and interventions. Biol Open 2016; 5:908-20. [PMID: 27288508 PMCID: PMC4958279 DOI: 10.1242/bio.019273] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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] [Indexed: 12/27/2022] Open
Abstract
Charcot–Marie–Tooth disease encompasses a genetically heterogeneous class of heritable polyneuropathies that result in axonal degeneration in the peripheral nervous system. Charcot–Marie–Tooth type 2D neuropathy (CMT2D) is caused by dominant mutations in glycyl tRNA synthetase (GARS). Mutations in the mouse Gars gene result in a genetically and phenotypically valid animal model of CMT2D. How mutations in GARS lead to peripheral neuropathy remains controversial. To identify putative disease mechanisms, we compared metabolites isolated from the spinal cord of Gars mutant mice and their littermate controls. A profile of altered metabolites that distinguish the affected and unaffected tissue was determined. Ascorbic acid was decreased fourfold in the spinal cord of CMT2D mice, but was not altered in serum. Carnitine and its derivatives were also significantly reduced in spinal cord tissue of mutant mice, whereas glycine was elevated. Dietary supplementation with acetyl-L-carnitine improved gross motor performance of CMT2D mice, but neither acetyl-L-carnitine nor glycine supplementation altered the parameters directly assessing neuropathy. Other metabolite changes suggestive of liver and kidney dysfunction in the CMT2D mice were validated using clinical blood chemistry. These effects were not secondary to the neuromuscular phenotype, as determined by comparison with another, genetically unrelated mouse strain with similar neuromuscular dysfunction. However, these changes do not seem to be causative or consistent metabolites of CMT2D, because they were not observed in a second mouse Gars allele or in serum samples from CMT2D patients. Therefore, the metabolite ‘fingerprint’ we have identified for CMT2D improves our understanding of cellular biochemical changes associated with GARS mutations, but identification of efficacious treatment strategies and elucidation of the disease mechanism will require additional studies. Summary: A metabolomics analysis of a mouse model of Charcot–Marie–Tooth type 2D neuropathy revealed a clear distinction between mutant and control samples, and the therapeutic potential of a subset of these changes was explored.
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Affiliation(s)
- Preeti Bais
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA
| | | | - Kathryn H Morelli
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA Graduate School of Biomedical Science and Engineering, University of Maine, Orono, 04469 ME, USA
| | | | | | - Alexei V Evsikov
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA Department of Molecular Medicine, USF Health, University of South Florida, Tampa, 33620 FL, USA
| | | | | | | | - Ivo Kremensky
- National Genetics Laboratory, Department of Obstetrics and Gynecology, University Hospital of Obstetrics and Gynecology, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Albena Jordanova
- Molecular Neurogenomics Group, VIB Department of Molecular Genetics, University of Antwerp, 2610 Antwerpen, Belgium Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA
| | - Robert W Burgess
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA Graduate School of Biomedical Science and Engineering, University of Maine, Orono, 04469 ME, USA
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12
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Quanbeck SM, Brachova L, Campbell AA, Guan X, Perera A, He K, Rhee SY, Bais P, Dickerson JA, Dixon P, Wohlgemuth G, Fiehn O, Barkan L, Lange I, Lange BM, Lee I, Cortes D, Salazar C, Shuman J, Shulaev V, Huhman DV, Sumner LW, Roth MR, Welti R, Ilarslan H, Wurtele ES, Nikolau BJ. Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of "Unknown Function". Front Plant Sci 2012; 3:15. [PMID: 22645570 PMCID: PMC3355754 DOI: 10.3389/fpls.2012.00015] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 01/17/2012] [Indexed: 05/19/2023]
Abstract
Metabolomics is the methodology that identifies and measures global pools of small molecules (of less than about 1,000 Da) of a biological sample, which are collectively called the metabolome. Metabolomics can therefore reveal the metabolic outcome of a genetic or environmental perturbation of a metabolic regulatory network, and thus provide insights into the structure and regulation of that network. Because of the chemical complexity of the metabolome and limitations associated with individual analytical platforms for determining the metabolome, it is currently difficult to capture the complete metabolome of an organism or tissue, which is in contrast to genomics and transcriptomics. This paper describes the analysis of Arabidopsis metabolomics data sets acquired by a consortium that includes five analytical laboratories, bioinformaticists, and biostatisticians, which aims to develop and validate metabolomics as a hypothesis-generating functional genomics tool. The consortium is determining the metabolomes of Arabidopsis T-DNA mutant stocks, grown in standardized controlled environment optimized to minimize environmental impacts on the metabolomes. Metabolomics data were generated with seven analytical platforms, and the combined data is being provided to the research community to formulate initial hypotheses about genes of unknown function (GUFs). A public database (www.PlantMetabolomics.org) has been developed to provide the scientific community with access to the data along with tools to allow for its interactive analysis. Exemplary datasets are discussed to validate the approach, which illustrate how initial hypotheses can be generated from the consortium-produced metabolomics data, integrated with prior knowledge to provide a testable hypothesis concerning the functionality of GUFs.
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Affiliation(s)
- Stephanie M. Quanbeck
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Libuse Brachova
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Alexis A. Campbell
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Xin Guan
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Ann Perera
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Kun He
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
| | - Seung Y. Rhee
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
| | - Preeti Bais
- Bioinformatics and Computational Biology Program, Iowa State UniversityAmes, IA, USA
| | - Julie A. Dickerson
- Bioinformatics and Computational Biology Program, Iowa State UniversityAmes, IA, USA
| | - Philip Dixon
- Department of Statistics, Iowa State UniversityAmes, IA, USA
| | | | - Oliver Fiehn
- Genome Center, University of CaliforniaDavis, CA, USA
| | - Lenore Barkan
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | - Iris Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | - B. Markus Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei UniversitySeoul, Korea
| | - Diego Cortes
- Anatomy and Neurobiology, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Carolina Salazar
- Department of Biological Sciences, University of North TexasDenton, TX, USA
| | - Joel Shuman
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North TexasDenton, TX, USA
| | - David V. Huhman
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Lloyd W. Sumner
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Mary R. Roth
- Division of Biology, Kansas State UniversityManhattan, KS, USA
| | - Ruth Welti
- Division of Biology, Kansas State UniversityManhattan, KS, USA
| | - Hilal Ilarslan
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Eve S. Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Basil J. Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
- *Correspondence: Basil J. Nikolau, Iowa State University, 3254 Molecular Biology Building, Ames, IA 50011, USA. e-mail:
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13
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Bais P, Moon-Quanbeck SM, Nikolau BJ, Dickerson JA. Plantmetabolomics.org: mass spectrometry-based Arabidopsis metabolomics--database and tools update. Nucleic Acids Res 2012; 40:D1216-20. [PMID: 22080512 PMCID: PMC3245150 DOI: 10.1093/nar/gkr969] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/13/2011] [Accepted: 10/14/2011] [Indexed: 11/13/2022] Open
Abstract
The PlantMetabolomics (PM) database (http://www.plantmetabolomics.org) contains comprehensive targeted and untargeted mass spectrum metabolomics data for Arabidopsis mutants across a variety of metabolomics platforms. The database allows users to generate hypotheses about the changes in metabolism for mutants with genes of unknown function. Version 2.0 of PlantMetabolomics.org currently contains data for 140 mutant lines along with the morphological data. A web-based data analysis wizard allows researchers to select preprocessing and data-mining procedures to discover differences between mutants. This community resource enables researchers to formulate models of the metabolic network of Arabidopsis and enhances the research community's ability to formulate testable hypotheses concerning gene functions. PM features new web-based tools for data-mining analysis, visualization tools and enhanced cross links to other databases. The database is publicly available. PM aims to provide a hypothesis building platform for the researchers interested in any of the mutant lines or metabolites.
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Affiliation(s)
- Preeti Bais
- Bioinformatics and Computational Biology Program, Electrical and Computer Engineering Department, Department of Biochemistry, Biophysics and Molecular Biology and Virtual Reality Application Center, Iowa State University, Ames, IA 50011, USA
| | - Stephanie M. Moon-Quanbeck
- Bioinformatics and Computational Biology Program, Electrical and Computer Engineering Department, Department of Biochemistry, Biophysics and Molecular Biology and Virtual Reality Application Center, Iowa State University, Ames, IA 50011, USA
| | - Basil J. Nikolau
- Bioinformatics and Computational Biology Program, Electrical and Computer Engineering Department, Department of Biochemistry, Biophysics and Molecular Biology and Virtual Reality Application Center, Iowa State University, Ames, IA 50011, USA
| | - Julie A. Dickerson
- Bioinformatics and Computational Biology Program, Electrical and Computer Engineering Department, Department of Biochemistry, Biophysics and Molecular Biology and Virtual Reality Application Center, Iowa State University, Ames, IA 50011, USA
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14
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Bais P, Moon SM, He K, Leitao R, Dreher K, Walk T, Sucaet Y, Barkan L, Wohlgemuth G, Roth MR, Wurtele ES, Dixon P, Fiehn O, Lange BM, Shulaev V, Sumner LW, Welti R, Nikolau BJ, Rhee SY, Dickerson JA. PlantMetabolomics.org: a web portal for plant metabolomics experiments. Plant Physiol 2010; 152:1807-16. [PMID: 20147492 PMCID: PMC2850039 DOI: 10.1104/pp.109.151027] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 02/08/2010] [Indexed: 05/20/2023]
Abstract
PlantMetabolomics.org (PM) is a web portal and database for exploring, visualizing, and downloading plant metabolomics data. Widespread public access to well-annotated metabolomics datasets is essential for establishing metabolomics as a functional genomics tool. PM integrates metabolomics data generated from different analytical platforms from multiple laboratories along with the key visualization tools such as ratio and error plots. Visualization tools can quickly show how one condition compares to another and which analytical platforms show the largest changes. The database tries to capture a complete annotation of the experiment metadata along with the metabolite abundance databased on the evolving Metabolomics Standards Initiative. PM can be used as a platform for deriving hypotheses by enabling metabolomic comparisons between genetically unique Arabidopsis (Arabidopsis thaliana) populations subjected to different environmental conditions. Each metabolite is linked to relevant experimental data and information from various annotation databases. The portal also provides detailed protocols and tutorials on conducting plant metabolomics experiments to promote metabolomics in the community. PM currently houses Arabidopsis metabolomics data generated by a consortium of laboratories utilizing metabolomics to help elucidate the functions of uncharacterized genes. PM is publicly available at http://www.plantmetabolomics.org.
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15
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Smith SM, Eng RH, Bais P, Fan-Havard P, Tecson-Tumang F. Epidemiology of ciprofloxacin resistance among patients with methicillin-resistant Staphylococcus aureus. J Antimicrob Chemother 1990; 26:567-72. [PMID: 2254224 DOI: 10.1093/jac/26.4.567] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
During the first twelve months after ciprofloxacin was introduced for clinical use at our institution, 65 new patients were found to be either infected or colonized by methicillin-resistant Staphylococcus aureus (MRSA) which were also ciprofloxacin resistant (CR-MRSA). Only 18 of these patients (28%) had been previously exposed to this antibiotic. Nine (50%) of the 18 patients had received ciprofloxacin for treatment for a pathogen other than MRSA. Although the initial cases of colonization or infection with CR-MRSA can be directly related to ciprofloxacin use, many of the subsequent cases of colonization and infection were not the consequence of ciprofloxacin therapy but rather hospital transmission of existing CR-MRSA.
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Affiliation(s)
- S M Smith
- Microbiology Section, Department of Veterans Affairs Medical Center, East Orange, New Jersey 07019
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16
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Abstract
Leukamic blasts from 8 patients with different forms of acute leukaemia were investigated for their capability to produce colony stimulating factor. A second point of investigation was to detect inhibitory activity from the same blasts. The agar technique in its double layer modification was used with bone marrow from C57 Bl mice as target cell population. No single pattern of colony growth was observed. CSF production was absent or very low, when compared with CSF from normal mononuclear cells. However, blasts from 4 patients disclosed inhibition of colony growth. No certain relationship existed between the cytochemic type of leukaemia and the production of either activator or inhibitor of in vitro colony formation.
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