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Lombardi RL, Ramsey JS, Mahoney JE, MacCoss MJ, Heck ML, Slupsky CM. Longitudinal Transcriptomic, Proteomic, and Metabolomic Response of Citrus sinensis to Diaphorina citri Inoculation of Candidatus Liberibacter asiaticus. J Proteome Res 2024. [PMID: 38373055 DOI: 10.1021/acs.jproteome.3c00485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Huanglongbing (HLB) is a fatal citrus disease that is currently threatening citrus varieties worldwide. One putative causative agent, Candidatus Liberibacter asiaticus (CLas), is vectored by Diaphorina citri, known as the Asian citrus psyllid (ACP). Understanding the details of CLas infection in HLB disease has been hindered by its Candidatus nature and the inability to confidently detect it in diseased trees during the asymptomatic stage. To identify early changes in citrus metabolism in response to inoculation of CLas using its natural psyllid vector, leaves from Madam Vinous sweet orange (Citrus sinensis (L.) Osbeck) trees were exposed to CLas-positive ACP or CLas-negative ACP and longitudinally analyzed using transcriptomics (RNA sequencing), proteomics (liquid chromatography-tandem mass spectrometry; data available in Dryad: 10.25338/B83H1Z), and metabolomics (proton nuclear magnetic resonance). At 4 weeks postexposure (wpe) to psyllids, the initial HLB plant response was primarily to the ACP and, to a lesser extent, the presence or absence of CLas. Additionally, analysis of 4, 8, 12, and 16 wpe identified 17 genes and one protein as consistently differentially expressed between leaves exposed to CLas-positive ACP versus CLas-negative ACP. This study informs identification of early detection molecular targets and contributes to a broader understanding of vector-transmitted plant pathogen interactions.
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Affiliation(s)
- Rachel L Lombardi
- Department of Food Science and Technology, University of California Davis, Davis, California 95616, United States
| | - John S Ramsey
- Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, New York 14853, United States
| | - Jaclyn E Mahoney
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michelle L Heck
- Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, New York 14853, United States
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, United States
| | - Carolyn M Slupsky
- Department of Food Science and Technology, University of California Davis, Davis, California 95616, United States
- Department of Nutrition, University of California Davis, Davis, California 95616, United States
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Hasegawa Y, Otoki Y, McClorry S, Coates LC, Lombardi RL, Taha AY, Slupsky CM. Optimization of a Method for the Simultaneous Extraction of Polar and Non-Polar Oxylipin Metabolites, DNA, RNA, Small RNA, and Protein from a Single Small Tissue Sample. Methods Protoc 2020; 3:mps3030061. [PMID: 32859006 PMCID: PMC7564281 DOI: 10.3390/mps3030061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 12/25/2022] Open
Abstract
A more comprehensive picture of tissue biology can be obtained through the application and integration of multiple omic technologies. However, the common challenge in working with a precious sample is having a sample too small to separately extract analytes of interest for each experiment. Considering the high heterogeneity that can be present in a single tissue sample, extracting all biomolecules from a single and undivided tissue is preferable because it allows direct comparison of results. Here, we combined a modified Folch extraction method with DNA, RNA, small RNA, and protein extraction using two commercial kits, which allowed us to extract polar metabolites and non-polar oxylipin metabolites, DNA, RNA, small RNA, and protein simultaneously from a small tissue sample. The method was validated in terms of quantity and quality of analytes for downstream analyses.
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Affiliation(s)
- Yu Hasegawa
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
| | - Yurika Otoki
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan
| | - Shannon McClorry
- Department of Nutrition, University of California-Davis, Davis, CA 95616, USA;
| | - Laurynne C. Coates
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
| | - Rachel L. Lombardi
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
| | - Ameer Y. Taha
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
| | - Carolyn M. Slupsky
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA; (Y.H.); (Y.O.); (L.C.C.); (R.L.L.); (A.Y.T.)
- Department of Nutrition, University of California-Davis, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-530-752-6804; Fax: +1-530-752-4759
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Van Dort ME, Hong H, Wang H, Nino CA, Lombardi RL, Blanks AE, Galbán S, Ross BD. Discovery of Bifunctional Oncogenic Target Inhibitors against Allosteric Mitogen-Activated Protein Kinase (MEK1) and Phosphatidylinositol 3-Kinase (PI3K). J Med Chem 2016; 59:2512-22. [PMID: 26943489 DOI: 10.1021/acs.jmedchem.5b01655] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The synthesis of a series of single entity, bifunctional MEK1/PI3K inhibitors achieved by covalent linking of structural analogs of the ATP-competitive PI3K inhibitor ZSTK474 and the ATP-noncompetitive MEK inhibitor PD0325901 is described. Inhibitors displayed potent in vitro inhibition of MEK1 (0.015 < IC50 (nM) < 56.7) and PI3K (54 < IC50 (nM) < 341) in enzymatic inhibition assays. Concurrent MEK1 and PI3K inhibition was demonstrated with inhibitors 9 and 14 in two tumor cell lines (A549, D54). Inhibitors produced dose-dependent decreased cell viability similar to the combined administration of equivalent doses of ZSTK474 and PD0325901. In vivo efficacy of 14 following oral administration was demonstrated in D54 glioma and A549 lung tumor bearing mice. Compound 14 showed a 95% and 67% inhibition of tumor ERK1/2 and Akt phosphorylation, respectively, at 2 h postadministration by Western blot analysis, confirming the bioavailability and efficacy of this bifunctional inhibitor strategy toward combined MEK1/PI3K inhibition.
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Affiliation(s)
- Marcian E Van Dort
- Center for Molecular Imaging, ‡Department of Radiology, and §Department of Biological Chemistry, The University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Hao Hong
- Center for Molecular Imaging, ‡Department of Radiology, and §Department of Biological Chemistry, The University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Hanxiao Wang
- Center for Molecular Imaging, ‡Department of Radiology, and §Department of Biological Chemistry, The University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Charles A Nino
- Center for Molecular Imaging, ‡Department of Radiology, and §Department of Biological Chemistry, The University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Rachel L Lombardi
- Center for Molecular Imaging, ‡Department of Radiology, and §Department of Biological Chemistry, The University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Avery E Blanks
- Center for Molecular Imaging, ‡Department of Radiology, and §Department of Biological Chemistry, The University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Stefanie Galbán
- Center for Molecular Imaging, ‡Department of Radiology, and §Department of Biological Chemistry, The University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Brian D Ross
- Center for Molecular Imaging, ‡Department of Radiology, and §Department of Biological Chemistry, The University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
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