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Chang A, Chakiryan NH, Du D, Stewart PA, Zhang Y, Tian Y, Soupir AC, Bowers K, Fang B, Morganti A, Teer JK, Kim Y, Spiess PE, Chahoud J, Noble JD, Putney RM, Berglund AE, Robinson TJ, Koomen JM, Wang L, Manley BJ. Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma. Eur Urol 2022; 82:354-362. [PMID: 35718636 PMCID: PMC11075093 DOI: 10.1016/j.eururo.2022.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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] [Received: 01/13/2022] [Revised: 04/24/2022] [Accepted: 05/24/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Alternative mRNA splicing can be dysregulated in cancer, resulting in the generation of aberrant splice variants (SVs). Given the paucity of actionable genomic mutations in clear cell renal cell carcinoma (ccRCC), aberrant SVs may be an avenue to novel mechanisms of pathogenesis. OBJECTIVE To identify and characterize aberrant SVs enriched in ccRCC. DESIGN, SETTING, AND PARTICIPANTS Using RNA-seq data from the Cancer Cell Line Encyclopedia, we identified neojunctions uniquely expressed in ccRCC. Candidate SVs were then checked for expression across normal tissue in the Genotype-Tissue Expression Project and primary tumor tissue from The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and our institutional Total Cancer Care database. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Clinicopathologic, genomic, and survival data were available for all cohorts. Epigenetic data were available for the TCGA and CPTAC cohorts. Proteomic data were available for the CPTAC cohort. The association of aberrant SV expression with these variables was examined using the Kruskal-Wallis test, pairwise t test, Spearman correlation test, and Cox regression analysis. RESULTS AND LIMITATIONS Our pipeline identified 16 ccRCC-enriched SVs. EGFR, HPCAL1-SV and RNASET2-SV expression was negatively correlated with gene-specific CpG methylation. We derived a survival risk score based primarily on the expression of five SVs (RNASET2, FGD1, PDZD2, COBLL1, and PTPN14), which was consistent and applicable across multiple cohorts on multivariate analysis. The splicing factor RBM4, which modulates splicing of HIF-1α, exhibited significantly lower expression at the protein level in the high-risk group, as defined by our SV-based score. CONCLUSIONS We describe 16 aberrant SVs enriched in ccRCC, many of which are associated with disease biology and/or clinical outcomes. This study provides a novel strategy for identifying and characterizing disease-specific aberrant SVs. PATIENT SUMMARY We describe a method to identify disease targets and biomarkers using transcriptomic analysis beyond somatic mutations or gene expression. Kidney tumors express unique splice variants that may provide additional prognostic information following surgery.
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Affiliation(s)
- Andrew Chang
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
| | - Nicholas H Chakiryan
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Dongliang Du
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Paul A Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Yonghong Zhang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Yijun Tian
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alex C Soupir
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA; Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Kiah Bowers
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Bin Fang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Ashley Morganti
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Youngchul Kim
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Philippe E Spiess
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jad Chahoud
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jerald D Noble
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA; Department of Radiation Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Ryan M Putney
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Anders E Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Timothy J Robinson
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - John M Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Brandon J Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA; Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
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Obermayer A, Dong L, Hu Q, Golden M, Noble JD, Rodriguez P, Robinson TJ, Teng M, Tan AC, Shaw TI. DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets. Biology (Basel) 2022; 11:260. [PMID: 35205126 PMCID: PMC8869715 DOI: 10.3390/biology11020260] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 01/10/2023]
Abstract
High-throughput transcriptomic and proteomic analyses are now routinely applied to study cancer biology. However, complex omics integration remains challenging and often time-consuming. Here, we developed DRPPM-EASY, an R Shiny framework for integrative multi-omics analysis. We applied our application to analyze RNA-seq data generated from a USP7 knockdown in T-cell acute lymphoblastic leukemia (T-ALL) cell line, which identified upregulated expression of a TAL1-associated proliferative signature in T-cell acute lymphoblastic leukemia cell lines. Next, we performed proteomic profiling of the USP7 knockdown samples. Through DRPPM-EASY-Integration, we performed a concurrent analysis of the transcriptome and proteome and identified consistent disruption of the protein degradation machinery and spliceosome in samples with USP7 silencing. To further illustrate the utility of the R Shiny framework, we developed DRPPM-EASY-CCLE, a Shiny extension preloaded with the Cancer Cell Line Encyclopedia (CCLE) data. The DRPPM-EASY-CCLE app facilitates the sample querying and phenotype assignment by incorporating meta information, such as genetic mutation, metastasis status, sex, and collection site. As proof of concept, we verified the expression of TP53 associated DNA damage signature in TP53 mutated ovary cancer cells. Altogether, our open-source application provides an easy-to-use framework for omics exploration and discovery.
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Affiliation(s)
- Alyssa Obermayer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (A.O.); (M.T.); (A.-C.T.)
| | - Li Dong
- Computational Biology Department, St Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Qianqian Hu
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL 33612, USA;
| | | | - Jerald D. Noble
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA; (J.D.N.); (T.J.R.)
| | - Paulo Rodriguez
- Department of Immunology, Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Timothy J. Robinson
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA; (J.D.N.); (T.J.R.)
| | - Mingxiang Teng
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (A.O.); (M.T.); (A.-C.T.)
| | - Aik-Choon Tan
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (A.O.); (M.T.); (A.-C.T.)
| | - Timothy I. Shaw
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (A.O.); (M.T.); (A.-C.T.)
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Carneiro CM, Noble JD, Pietras A, Moler P, Austin JD. Iso-seq analysis and functional annotation of the Santa Fe cave crayfish (Procambarus erythrops) transcriptome. Mar Genomics 2021; 58:100842. [PMID: 34217485 DOI: 10.1016/j.margen.2021.100842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 10/22/2022]
Abstract
The genus Procambarus represents a diverse genus of freshwater crayfish that includes epigean species, stygobitic species, and at least one parthenogenic species. Despite its evolutionary, ecological, and economic importance, most genomic and transcriptomic resources for this genus are limited to a couple of model species. We sequenced the transcriptome of a non-model species, P. erythrops, a geographically restricted stygobitic species from Florida. RNA isolated from gill, muscle and eye tissue was pooled to create a de novo transcriptome assembly using Single Molecule Real-Time sequencing (PacBio), resulting in 19,442 full-length isoforms. The assembly has been deposited in the NCBI (BioProject PRJNA657230). These data will make an important contribution to the comparative study of transcriptome evolution in crayfish and crustaceans.
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Affiliation(s)
- Celine M Carneiro
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, United States of America; School of Natural Resources and Environment, University of Florida, Gainesville, FL 32611, United States of America
| | - Jerald D Noble
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611, United States of America
| | - Adele Pietras
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, United States of America
| | - Paul Moler
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Insituute, 1105 SW Williston Road, Gainesville FL32601, United States of America
| | - James D Austin
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, United States of America; School of Natural Resources and Environment, University of Florida, Gainesville, FL 32611, United States of America.
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Kong W, Yoo MJ, Zhu D, Noble JD, Kelley TM, Li J, Kirst M, Assmann SM, Chen S. Molecular changes in Mesembryanthemum crystallinum guard cells underlying the C 3 to CAM transition. Plant Mol Biol 2020; 103:653-667. [PMID: 32468353 DOI: 10.1007/s11103-020-01016-9] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 05/17/2020] [Indexed: 05/14/2023]
Abstract
KEY MESSAGE: The timing and transcriptomic changes during the C3 to CAM transition of common ice plant support the notion that guard cells themselves can shift from C3 to CAM. Crassulacean acid metabolism (CAM) is a specialized type of photosynthesis: stomata close during the day, enhancing water conservation, and open at night, allowing CO2 uptake. Mesembryanthemum crystallinum (common ice plant) is a facultative CAM species that can shift from C3 photosynthesis to CAM under salt or drought stresses. However, the molecular mechanisms underlying the stress induced transition from C3 to CAM remain unknown. Here we determined the transition time from C3 to CAM in M. crystallinum under salt stress. In parallel, single-cell-type transcriptomic profiling by 3'-mRNA sequencing was conducted in isolated stomatal guard cells to determine the molecular changes in this key cell type during the transition. In total, 495 transcripts showed differential expression between control and salt-treated samples during the transition, including 285 known guard cell genes, seven CAM-related genes, 18 transcription factors, and 185 other genes previously not found to be expressed in guard cells. PEPC1 and PPCK1, which encode key enzymes of CAM photosynthesis, were up-regulated in guard cells after seven days of salt treatment, indicating that guard cells themselves can shift from C3 to CAM. This study provides important information towards introducing CAM stomatal behavior into C3 crops to enhance water use efficiency.
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Affiliation(s)
- Wenwen Kong
- College of Life Sciences, Northeast Agricultural University, Harbin, China
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
- Guangdong Province Key Laboratory for Plant Epigenetics, College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Mi-Jeong Yoo
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
| | - Dan Zhu
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
- College of Life Science, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, China
| | - Jerald D Noble
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - Theresa M Kelley
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
| | - Jing Li
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA.
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, USA.
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA.
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Balmant KM, Noble JD, C Alves F, Dervinis C, Conde D, Schmidt HW, Vazquez AI, Barbazuk WB, Campos GDL, Resende MFR, Kirst M. Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides. Genome Res 2020; 30:1131-1143. [PMID: 32817237 PMCID: PMC7462072 DOI: 10.1101/gr.261438.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/13/2020] [Indexed: 02/01/2023]
Abstract
Despite the growing resources and tools for high-throughput characterization and analysis of genomic information, the discovery of the genetic elements that regulate complex traits remains a challenge. Systems genetics is an emerging field that aims to understand the flow of biological information that underlies complex traits from genotype to phenotype. In this study, we used a systems genetics approach to identify and evaluate regulators of the lignin biosynthesis pathway in Populus deltoides by combining genome, transcriptome, and phenotype data from a population of 268 unrelated individuals of P. deltoides The discovery of lignin regulators began with the quantitative genetic analysis of the xylem transcriptome and resulted in the detection of 6706 and 4628 significant local- and distant-eQTL associations, respectively. Among the locally regulated genes, we identified the R2R3-MYB transcription factor MYB125 (Potri.003G114100) as a putative trans-regulator of the majority of genes in the lignin biosynthesis pathway. The expression of MYB125 in a diverse population positively correlated with lignin content. Furthermore, overexpression of MYB125 in transgenic poplar resulted in increased lignin content, as well as altered expression of genes in the lignin biosynthesis pathway. Altogether, our findings indicate that MYB125 is involved in the control of a transcriptional coexpression network of lignin biosynthesis genes during secondary cell wall formation in P. deltoides.
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Affiliation(s)
- Kelly M Balmant
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA
| | - Jerald D Noble
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611, USA
| | - Filipe C Alves
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824, USA
| | - Christopher Dervinis
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA
| | - Daniel Conde
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA
| | - Henry W Schmidt
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA
| | - Ana I Vazquez
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824, USA
| | - William B Barbazuk
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Gustavo de Los Campos
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824, USA
- Statistics Department, Michigan State University, East Lansing, Michigan 48824, USA
| | - Marcio F R Resende
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611, USA
- Horticulture Sciences Department, University of Florida, Gainesville, Florida 32611, USA
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
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Noble JD, Balmant KM, Dervinis C, de los Campos G, Resende MFR, Kirst M, Barbazuk WB. The Genetic Regulation of Alternative Splicing in Populus deltoides. Front Plant Sci 2020; 11:590. [PMID: 32582229 PMCID: PMC7291814 DOI: 10.3389/fpls.2020.00590] [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] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Alternative splicing (AS) is a mechanism of regulation of the proteome via enabling the production of multiple mRNAs from a single gene. To date, the dynamics of AS and its effects on the protein sequences of individuals in a large and genetically unrelated population of trees have not been investigated. Here we describe the diversity of AS events within a previously genotyped population of 268 individuals of Populus deltoides and their putative downstream functional effects. Using a robust bioinformatics pipeline, the AS events and resulting transcript isoforms were discovered and quantified for each individual in the population. Analysis of the AS revealed that, as expected, most AS isoforms are conserved. However, we also identified a substantial collection of new, unannotated splice junctions and transcript isoforms. Heritability estimates for the expression of transcript isoforms showed that approximately half of the isoforms are heritable. The genetic regulators of these AS isoforms and splice junction usage were then identified using a genome-wide association analysis. The expression of AS isoforms was predominately cis regulated while splice junction usage was generally regulated in trans. Additionally, we identified 696 genes encoding alternatively spliced isoforms that changed putative protein domains relative to the longest protein coding isoform of the gene, and 859 genes exhibiting this same phenomenon relative to the most highly expressed isoform. Finally, we found that 748 genes gained or lost micro-RNA binding sites relative to the longest protein coding isoform of a given gene, while 940 gained or lost micro-RNA binding sites relative to the most highly expressed isoform. These results indicate that a significant fraction of AS events are genetically regulated and that this isoform usage can result in protein domain architecture changes.
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Affiliation(s)
- Jerald D. Noble
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
| | - Kelly M. Balmant
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | - Christopher Dervinis
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | - Gustavo de los Campos
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, United States
| | - Márcio F. R. Resende
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
| | - Matias Kirst
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - William Brad Barbazuk
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
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Kang SH, Sun YD, Atallah OO, Huguet-Tapia JC, Noble JD, Folimonova SY. A Long Non-Coding RNA of Citrus tristeza virus: Role in the Virus Interplay with the Host Immunity. Viruses 2019; 11:E436. [PMID: 31091710 PMCID: PMC6563247 DOI: 10.3390/v11050436] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/08/2019] [Accepted: 05/11/2019] [Indexed: 01/01/2023] Open
Abstract
During infection, Citrus tristeza virus (CTV) produces a non-coding subgenomic RNA referred to as low-molecular-weight tristeza 1 (LMT1), which for a long time has been considered as a by-product of the complex CTV replication machinery. In this study, we investigated the role of LMT1 in the virus infection cycle using a CTV variant that does not produce LMT1 (CTV-LMT1d). We showed that lack of LMT1 did not halt virus ability to replicate or form proper virions. However, the mutant virus demonstrated significantly reduced invasiveness and systemic spread in Nicotiana benthamiana as well as an inability to establish infection in citrus. Introduction of CTV-LMT1d into the herbaceous host resulted in elevation of the levels of salicylic acid (SA) and SA-responsive pathogenesis-related genes beyond those upon inoculation with wild-type (WT) virus (CTV-WT). Further analysis showed that the LMT1 RNA produced by CTV-WT or via ectopic expression in the N. benthamiana leaves suppressed SA accumulation and up-regulated an alternative oxidase gene, which appeared to mitigate the accumulation of reactive oxygen species. To the best of our knowledge, this is the first report of a plant viral long non-coding RNA being involved in counter-acting host response by subverting the SA-mediated plant defense.
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Affiliation(s)
- Sung-Hwan Kang
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | - Yong-Duo Sun
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
| | - Osama O Atallah
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | | | - Jerald D Noble
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
| | - Svetlana Y Folimonova
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
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Noble JD, Farrell PA. Effect of exercise training on the onset of type I diabetes in the BB/Wor rat. Med Sci Sports Exerc 1994; 26:1130-4. [PMID: 7808247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The effects of regular exercise training on the onset and/or severity of hyperglycemia were studied in female diabetes-prone Biobreeding/Worcester (DP BB/Wor) rats. At 38-39 d of age, animals were weight-matched and randomly assigned to exercise-trained (T) and untrained (Unt) groups. The T rats exercised on a rodent treadmill at a moderate workload, 5 successive days with the 6th day being one of rest. Training lasted 5-11 wk until rats became moribund. Red gastrocnemius muscle citrate synthase activity was significantly higher in T (54.2 +/- 4.7 mumol.g-1.min-1) compared with Unt (42.9 +/- 5.1). No significant difference was found between the T and Unt groups in the following: age at onset of hyperglycemia (T = 82.9 +/- 8.7 d; Unt = 82.0 +/- 13.5 d, mean +/- SD), ultimate level of hyperglycemia, age of death (T = 89.9 +/- 9.2 d; Unt = 89.4 +/- 13.9 d), number of days between onset of hyperglycemia and death, or body weights at the onset of hyperglycemia. No significant difference was found between groups in pancreatic insulin concentration (microgram.g-1 of protein), T = 0.22 +/- 0.04; Unt = 0.20 +/- 0.34. These data suggest that a program of regular exercise training may not delay the onset and/or reduce the severity of hyperglycemia in the DP BB/Wor rat. Regular exercise training had no beneficial or detrimental effect on pancreatic beta-cell destruction.
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Affiliation(s)
- J D Noble
- Noll Physiological Research Center, Pennsylvania State University, University Park 16802
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