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Roberts BR, Laffoon SB, Roberts AM, Porter T, Fowler C, Masters CL, Dratz EA, Laws SM. Discovery of a Missense Mutation (Q222K) of the APOE Gene from the Australian Imaging, Biomarker and Lifestyle Study. J Alzheimers Dis Rep 2023; 7:165-172. [PMID: 36891255 PMCID: PMC9986708 DOI: 10.3233/adr-220075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023] Open
Abstract
After age, polymorphisms of the Apolipoprotein E (APOE) gene are the biggest risk factor for the development of Alzheimer's disease (AD). During our investigation to discovery biomarkers in plasma, using 2D gel electrophoresis, we found an individual with and unusual apoE isoelectric point compared to APOE ɛ2, ɛ3, and ɛ4 carriers. Whole exome sequencing of APOE from the donor confirmed a single nucleotide polymorphism (SNP) in exon 4, translating to a rare Q222K missense mutation. The apoE ɛ4 (Q222K) mutation did not form dimers or complexes observed for apoE ɛ2 & ɛ3 proteins.
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Affiliation(s)
- Blaine R Roberts
- Emory School of Medicine, Department of Biochemistry, Department of Neurology, Atlanta, GA, USA.,Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Scott B Laffoon
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Anne M Roberts
- Emory School of Medicine, Department of Biochemistry, Department of Neurology, Atlanta, GA, USA.,Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.,Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Chris Fowler
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Colin L Masters
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Edward A Dratz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Simon M Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.,Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
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Laffoon SB, Doecke JD, Roberts AM, Vance JA, Reeves BD, Pertile KK, Rumble RL, Fowler CJ, Trounson B, Ames D, Martins R, Bush AI, Masters CL, Grieco PA, Dratz EA, Roberts BR. Analysis of plasma proteins using 2D gels and novel fluorescent probes: in search of blood based biomarkers for Alzheimer's disease. Proteome Sci 2022; 20:2. [PMID: 35081972 PMCID: PMC8790928 DOI: 10.1186/s12953-021-00185-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The Australian Imaging and Biomarker Lifestyle (AIBL) study of aging is designed to aid the discovery of biomarkers. The current study aimed to discover differentially expressed plasma proteins that could yield a blood-based screening tool for Alzheimer's disease. METHODS The concentration of proteins in plasma covers a vast range of 12 orders of magnitude. Therefore, to search for medium to low abundant biomarkers and elucidate mechanisms of AD, we immuno-depleted the most abundant plasma proteins and pre-fractionated the remaining proteins by HPLC, prior to two-dimensional gel electrophoresis. The relative levels of approximately 3400 protein species resolved on the 2D gels were compared using in-gel differential analysis with spectrally resolved fluorescent protein detection dyes (Zdyes™). Here we report on analysis of pooled plasma samples from an initial screen of a sex-matched cohort of 72 probable AD patients and 72 healthy controls from the baseline time point of AIBL. RESULTS We report significant changes in variants of apolipoprotein E, haptoglobin, α1 anti-trypsin, inter-α trypsin inhibitor, histidine-rich glycoprotein, and a protein of unknown identity. α1 anti-trypsin and α1 anti-chymotrypsin demonstrated plasma concentrations that were dependent on APOE ε4 allele dose. Our analysis also identified an association with the level of Vitamin D binding protein fragments and complement factor I with sex. We then conducted a preliminary validation study, on unique individual samples compared to the discovery cohort, using a targeted LC-MS/MS assay on a subset of discovered biomarkers. We found that targets that displayed a high degree of isoform specific changes in the 2D gels were not changed in the targeted MS assay which reports on the total level of the biomarker. CONCLUSIONS This demonstrates that further development of mass spectrometry assays is needed to capture the isoform complexity that exists in theses biological samples. However, this study indicates that a peripheral protein signature has potential to aid in the characterization of AD.
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Affiliation(s)
- Scott B. Laffoon
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715 USA
- Cooperative Research Centre for Mental Health, Carlton South, VIC Australia
| | - James D. Doecke
- Australian e-Health Research Centre, CSIRO and Cooperative Research Centre of Mental Health, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029 Australia
| | - Anne M. Roberts
- Department of Biochemistry, Emory School of Medicine, 4001 Rollins Research Building, Atlanta, GA 30322 USA
- Department of Neurology, Emory School of Medicine, 4001 Rollins Research Building, Atlanta, GA 30322 USA
| | | | - Benjamin D. Reeves
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715 USA
| | - Kelly K. Pertile
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
| | - Rebecca L. Rumble
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
| | - Chris J. Fowler
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
| | - Brett Trounson
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
| | - David Ames
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
| | - Ralph Martins
- Cooperative Research Centre for Mental Health, Carlton South, VIC Australia
- School of Medical Sciences, Edith Cowan University, Joondalup, WA Australia
- Department of Biomedical Sciences, Macquarie University, North Ryde, NSW Australia
| | - Ashley I. Bush
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
- Cooperative Research Centre for Mental Health, Carlton South, VIC Australia
| | - Colin L. Masters
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
- Cooperative Research Centre for Mental Health, Carlton South, VIC Australia
| | - Paul A. Grieco
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715 USA
| | - Edward A. Dratz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715 USA
| | - Blaine R. Roberts
- Department of Biochemistry, Emory School of Medicine, 4001 Rollins Research Building, Atlanta, GA 30322 USA
- Department of Neurology, Emory School of Medicine, 4001 Rollins Research Building, Atlanta, GA 30322 USA
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Macdonald PJ, Gayda S, Haack RA, Ruan Q, Himmelsbach RJ, Tetin SY. Rhodamine-Derived Fluorescent Dye with Inherent Blinking Behavior for Super-Resolution Imaging. Anal Chem 2018; 90:9165-9173. [DOI: 10.1021/acs.analchem.8b01645] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Patrick J. Macdonald
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Susan Gayda
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Richard A. Haack
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Qiaoqiao Ruan
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Richard J. Himmelsbach
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Sergey Y. Tetin
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois 60064, United States
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Roubinet B, Bischoff M, Nizamov S, Yan S, Geisler C, Stoldt S, Mitronova GY, Belov VN, Bossi ML, Hell SW. Photoactivatable Rhodamine Spiroamides and Diazoketones Decorated with “Universal Hydrophilizer” or Hydroxyl Groups. J Org Chem 2018; 83:6466-6476. [DOI: 10.1021/acs.joc.8b00756] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benôit Roubinet
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Matthias Bischoff
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Shamil Nizamov
- Abberior GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Sergey Yan
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Claudia Geisler
- Department of Optical Nanoscopy, Laser-Laboratorium Göttingen e.V., 37077 Göttingen, Germany
| | - Stefan Stoldt
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Gyuzel Y. Mitronova
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Vladimir N. Belov
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Mariano L. Bossi
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan W. Hell
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Keith BK, Burns EE, Bothner B, Carey CC, Mazurie AJ, Hilmer JK, Biyiklioglu S, Budak H, Dyer WE. Intensive herbicide use has selected for constitutively elevated levels of stress-responsive mRNAs and proteins in multiple herbicide-resistant Avena fatua L. PEST MANAGEMENT SCIENCE 2017; 73:2267-2281. [PMID: 28485049 DOI: 10.1002/ps.4605] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/02/2017] [Accepted: 05/03/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND Intensive use of herbicides has led to the evolution of two multiple herbicide-resistant (MHR) Avena fatua (wild oat) populations in Montana that are resistant to members of all selective herbicide families available for A. fatua control in US small grain crops. We used transcriptome and proteome surveys to compare constitutive changes in MHR and herbicide-susceptible (HS) plants associated with non-target site resistance. RESULTS Compared to HS plants, MHR plants contained constitutively elevated levels of differentially expressed genes (DEGs) with functions in xenobiotic catabolism, stress response, redox maintenance and transcriptional regulation that are similar to abiotic stress-tolerant phenotypes. Proteome comparisons identified similarly elevated proteins including biosynthetic and multifunctional enzymes in MHR plants. Of 25 DEGs validated by RT-qPCR assay, differential regulation of 21 co-segregated with flucarbazone-sodium herbicide resistance in F3 families, and a subset of 10 of these were induced or repressed in herbicide-treated HS plants. CONCLUSION Although the individual and collective contributions of these DEGs and proteins to MHR remain to be determined, our results support the idea that intensive herbicide use has selected for MHR populations with altered, constitutively regulated patterns of gene expression that are similar to those in abiotic stress-tolerant plants. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Barbara K Keith
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Erin E Burns
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry Research, Montana State University, Bozeman, MT, USA
| | - Charles C Carey
- Research Cyberinfrastructure, Montana State University, Bozeman, MT, USA
| | - Aurélien J Mazurie
- Research Cyberinfrastructure, Montana State University, Bozeman, MT, USA
| | - Jonathan K Hilmer
- Information Technology Center, Montana State University, Bozeman, MT, USA
| | - Sezgi Biyiklioglu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - William E Dyer
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
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Burns EE, Keith BK, Refai MY, Bothner B, Dyer WE. Proteomic and biochemical assays of glutathione-related proteins in susceptible and multiple herbicide resistant Avena fatua L. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2017; 140:69-78. [PMID: 28755697 DOI: 10.1016/j.pestbp.2017.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/08/2017] [Accepted: 06/08/2017] [Indexed: 06/07/2023]
Abstract
Extensive herbicide usage has led to the evolution of resistant weed populations that cause substantial crop yield losses and increase production costs. The multiple herbicide resistant (MHR) Avena fatua L. populations utilized in this study are resistant to members of all selective herbicide families, across five modes of action, available for A. fatua control in U.S. small grain production, and thus pose significant agronomic and economic threats. Resistance to ALS and ACCase inhibitors is not conferred by target site mutations, indicating that non-target site resistance mechanisms are involved. To investigate the potential involvement of glutathione-related enzymes in the MHR phenotype, we used a combination of proteomic, biochemical, and immunological approaches to compare their constitutive activities in herbicide susceptible (HS1 and HS2) and MHR (MHR3 and MHR4) A. fatua plants. Proteomic analysis identified three tau and one phi glutathione S-transferases (GSTs) present at higher levels in MHR compared to HS plants, while immunoassays revealed elevated levels of lambda, phi, and tau GSTs. GST specific activity towards 1-chloro-2,4-dinitrobenzene was 1.2-fold higher in MHR4 than in HS1 plants and 1.3- and 1.2-fold higher in MHR3 than in HS1 and HS2 plants, respectively. However, GST specific activities towards fenoxaprop-P-ethyl and imazamethabenz-methyl were not different between untreated MHR and HS plants. Dehydroascorbate reductase specific activity was 1.4-fold higher in MHR than HS plants. Pretreatment with the GST inhibitor NBD-Cl did not affect MHR sensitivity to fenoxaprop-P-ethyl application, while the herbicide safener and GST inducer mefenpyr reduced the efficacy of low doses of fenoxaprop-P-ethyl on MHR4 but not MHR3 plants. Mefenpyr treatment also partially reduced the efficacy of thiencarbazone-methyl or mesosulfuron-methyl on MHR3 or MHR4 plants, respectively. Overall, the GSTs described here are not directly involved in enhanced rates of fenoxaprop-P-ethyl or imazamethabenz-methyl metabolism in MHR A. fatua. Instead, we propose that the constitutively elevated GST proteins and related enzymes in MHR plants are representative of a larger, more global suite of abiotic stress-related changes.
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Affiliation(s)
- Erin E Burns
- Department of Plant Sciences & Plant Pathology, PO Box 173150, Montana State University, Bozeman, MT 59717, United States
| | - Barbara K Keith
- Department of Plant Sciences & Plant Pathology, PO Box 173150, Montana State University, Bozeman, MT 59717, United States
| | - Mohammed Y Refai
- Department of Chemistry & Biochemistry Research, PO Box 173400, Montana State University, Bozeman, MT 59717, United States
| | - Brian Bothner
- Department of Chemistry & Biochemistry Research, PO Box 173400, Montana State University, Bozeman, MT 59717, United States
| | - William E Dyer
- Department of Plant Sciences & Plant Pathology, PO Box 173150, Montana State University, Bozeman, MT 59717, United States.
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Chen W, Xue M, Shea KJ, Meng Z, Yan Z, Wang Z, Xue F, Qu F. Molecularly imprinted hollow sphere array for the sensing of proteins. JOURNAL OF BIOPHOTONICS 2015; 8:838-45. [PMID: 25504746 DOI: 10.1002/jbio.201400100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/12/2014] [Accepted: 11/05/2014] [Indexed: 05/23/2023]
Abstract
Mono-dispersed molecularly imprinted hollow spheres (MIHSs) for hemoglobin (Hb) were prepared by employing silica nanospheres as the sacrificial templates. The obtained hollow spheres with uniform particle size of 360 nm in diameter were characterized by transmission electron microscopy. The outstanding affinities of these MIHSs to the target protein were confirmed by adsorption experiment in aqueous solution. Adsorption equilibrium was achieved within 10 min while the binding capacity (Qmax ) of Hb was 8.84 µmol g(-1) at pH7.0. Furthermore, the MIHSs were successfully assembled into a closely-packed 3D colloidal array. The molecularly imprinted hollow sphere array (MIHSA) can selectively recognize Hb. As the concentration of Hb increased, the structure color of the MIHSA changed from blue to green, and turn to white finally with maximum red shift for 43 nm. The MIHSA showed promising potential for the naked-eye detection of target Hb. Reflection spectra of the MIHSA in response to different Hb concentrations (0.075-15 µmol L(-1) ).
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Affiliation(s)
- Wei Chen
- School of Chemical Engineering & Environment, Beijing Institute of Technology, Beijing, 100081, P.R. China
| | - Min Xue
- School of Chemical Engineering & Environment, Beijing Institute of Technology, Beijing, 100081, P.R. China.
| | - Kenneth J Shea
- Department of Chemistry, University of California, Irvine, California, 92697, United States
| | - Zihui Meng
- School of Chemical Engineering & Environment, Beijing Institute of Technology, Beijing, 100081, P.R. China.
| | - Zequn Yan
- School of Chemical Engineering & Environment, Beijing Institute of Technology, Beijing, 100081, P.R. China
| | - Zhe Wang
- School of Chemical Engineering & Environment, Beijing Institute of Technology, Beijing, 100081, P.R. China
| | - Fei Xue
- School of Chemical Engineering & Environment, Beijing Institute of Technology, Beijing, 100081, P.R. China
| | - Feng Qu
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, P.R. China
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