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Chen ZZ, Dufresne J, Bowden P, Miao M, Marshall JG. Extraction of naturally occurring peptides versus the tryptic digestion of proteins from fetal versus adult bovine serum for LC-ESI-MS/MS. Anal Biochem 2024; 689:115497. [PMID: 38461948 DOI: 10.1016/j.ab.2024.115497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/12/2024]
Abstract
The naturally occurring peptides and digested proteins of fetal versus adult bovine serum were compared by LC-ESI-MS/MS after correction against noise from blank injections and random MS/MS spectra as statistical controls. Serum peptides were extracted by differential precipitation with mixtures of acetonitrile and water. Serum proteins were separated by partition chromatography over quaternary amine resin followed by tryptic digestion. The rigorous X!TANDEM goodness of fit algorithm that has a low error rate as demonstrated by low FDR q-values (q ≤ 0.01) showed qualitative and quantitative agreement with the SEQUEST cross correlation algorithm on 12,052 protein gene symbols. Tryptic digestion provided a quantitative identification of the serum proteins where observation frequency reflected known high abundance. In contrast, the naturally occurring peptides reflected the cleavage of common serum proteins such as C4A, C3, FGB, HPX, A2M but also proteins in lower concentration such as F13A1, IK, collagens and protocadherins. Proteins associated with cellular growth and development such as actins (ACT), ribosomal proteins like Ribosomal protein S6 (RPS6), synthetic enzymes and extracellular matrix factors were enriched in fetal calf serum. In contrast to the large literature from cord blood, IgG light chains were absent from fetal serum as observed by LC-ESI-MS/MS and confirmed by ELISA.
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Affiliation(s)
- Zhuo Zhen Chen
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Jaimie Dufresne
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Peter Bowden
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Ming Miao
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - John G Marshall
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
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Gopinath T, Shin K, Tian Y, Im W, Struppe J, Perrone B, Hassan A, Marassi FM. Solid-state NMR MAS CryoProbe enables structural studies of human blood protein vitronectin bound to hydroxyapatite. J Struct Biol 2024; 216:108061. [PMID: 38185342 PMCID: PMC10939839 DOI: 10.1016/j.jsb.2024.108061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The low sensitivity of nuclear magnetic resonance (NMR) is a major bottleneck for studying biomolecular structures of complex biomolecular assemblies. Cryogenically cooled probe technology overcomes the sensitivity limitations enabling NMR applications to challenging biomolecular systems. Here we describe solid-state NMR studies of the human blood protein vitronectin (Vn) bound to hydroxyapatite (HAP), the mineralized form of calcium phosphate, using a CryoProbe designed for magic angle spinning (MAS) experiments. Vn is a major blood protein that regulates many different physiological and pathological processes. The high sensitivity of the CryoProbe enabled us to acquire three-dimensional solid-state NMR spectra for sequential assignment and characterization of site-specific water-protein interactions that provide initial insights into the organization of the Vn-HAP complex. Vn associates with HAP in various pathological settings, including macular degeneration eyes and Alzheimer's disease brains. The ability to probe these assemblies at atomic detail paves the way for understanding their formation.
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Affiliation(s)
- T Gopinath
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kyungsoo Shin
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ye Tian
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, PA 18015, USA
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | | | - Alia Hassan
- Bruker Switzerland AG, Fallanden, Switzerland
| | - Francesca M Marassi
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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3
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Lin Y, Hu T, Cheng L, Chen Y, Li W, Guo Q, Miao Y. Causal Effects of Plasma Haptoglobin Levels on Alzheimer's Disease: A Two-Sample Mendelian Randomization Study. J Alzheimers Dis 2023; 95:339-348. [PMID: 37522206 DOI: 10.3233/jad-230159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
BACKGROUND A connection between plasma levels of haptoglobin (Hp) and Alzheimer's disease (AD) has been shown in several observational studies. It is debatable, nonetheless, how the two are related causally. OBJECTIVE To establish the causal relationship between Hp and AD using a two-sample Mendelian randomization (MR) study. METHODS From the extensive genome-wide association studies and FinnGen dataset, summaries and statistics pertaining to AD were gathered. We investigated the possibility of a causal link between Hp and AD using a two-sample MR study. Inverse variance weighting was used as the primary analytical technique, and it was supported by the joint application of complementary analyses and fixed effects meta-analysis to combine results from various sources. RESULTS Genetically determined Hp was causally associated with AD [odds ratio (OR), 1.05; 95% confidence interval (CI), 1.02 to 1.09; p = 8.96×10-4]; Inverse variance-weighted estimates coming from different data sources were combined in a meta-analysis with consistent findings (OR, 1.03; 95% CI, 1.01 to 1.05; p = 2.00×10-3). The outcomes of the inverse MR analysis showed that AD had no appreciable causal impact on Hp. CONCLUSION The present MR analysis shows that higher plasma Hp leads to an increased risk of AD. Strategies for plasma Hp testing may open up new doors for the early diagnosis and prevention of AD.
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Affiliation(s)
- Yijia Lin
- Department of Geriatrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tingjun Hu
- Department of Geriatrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lizhen Cheng
- Department of Geriatrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yixin Chen
- Department of Geriatrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Li
- Department of Geriatrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qihao Guo
- Department of Geriatrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ya Miao
- Department of Geriatrics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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4
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Rani S, Chandna P. Multiomics Analysis-Based Biomarkers in Diagnosis of Polycystic Ovary Syndrome. Reprod Sci 2023; 30:1-27. [PMID: 35084716 PMCID: PMC10010205 DOI: 10.1007/s43032-022-00863-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 01/20/2022] [Indexed: 01/06/2023]
Abstract
Polycystic ovarian syndrome is an utmost communal endocrine, psychological, reproductive, and metabolic disorder that occurs in women of reproductive age with extensive range of clinical manifestations. This may even lead to long-term multiple morbidities including obesity, diabetes mellitus, insulin resistance, cardiovascular disease, infertility, cerebrovascular diseases, and ovarian and endometrial cancer. Women affliction from PCOS in midst assemblage of manifestations allied with menstrual dysfunction and androgen exorbitance, which considerably affects eminence of life. PCOS is recognized as a multifactorial disorder and systemic syndrome in first-degree family members; therefore, the etiology of PCOS syndrome has not been copiously interpreted. The disorder of PCOS comprehends numerous allied health conditions and has influenced various metabolic processes. Due to multifaceted pathophysiology engaging several pathways and proteins, single genetic diagnostic tests cannot be supportive to determine in straight way. Clarification of cellular and biochemical pathways and various genetic players underlying PCOS could upsurge our consideration of pathophysiology of this syndrome. It is requisite to know pathophysiological relationship between biomarker and their reflection towards PCOS disease. Biomarkers deliver vibrantly and potent ways to apprehend the spectrum of PCOS with applications in screening, diagnosis, characterization, and monitoring. This paper relies on the endeavor to point out many candidates as potential biomarkers based on omics technologies, thus highlighting correlation between PCOS disease with innovative technologies. Therefore, the objective of existing review is to encapsulate more findings towards cutting-edge advances in prospective use of biomarkers for PCOS disease. Discussed biomarkers may be fruitful in guiding therapies, addressing disease risk, and predicting clinical outcomes in future.
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Affiliation(s)
- Shikha Rani
- Department of Biophysics, University of Delhi, South Campus, Benito Juarez Road, New Delhi , 110021, India.
| | - Piyush Chandna
- Natdynamics Biosciences Confederation, Gurgaon, Haryana, 122001, India
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5
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Tian Y, Shin K, Aleshin AE, Im W, Marassi FM. Calcium-induced environmental adaptability of the blood protein vitronectin. Biophys J 2022; 121:3896-3906. [PMID: 36056555 PMCID: PMC9674982 DOI: 10.1016/j.bpj.2022.08.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/29/2022] [Accepted: 08/29/2022] [Indexed: 11/22/2022] Open
Abstract
The adaptability of proteins to their work environments is fundamental for cellular life. Here, we describe how the hemopexin-like domain of the multifunctional blood glycoprotein vitronectin binds Ca2+ to adapt to excursions of temperature and shear stress. Using X-ray crystallography, molecular dynamics simulations, NMR, and differential scanning fluorimetry, we describe how Ca2+ and its flexible hydration shell enable the protein to perform conformational changes that relay beyond the calcium-binding site and alter the number of polar contacts to enhance conformational stability. By means of mutagenesis, we identify key residues that cooperate with Ca2+ to promote protein stability, and we show that calcium association confers protection against shear stress, a property that is advantageous for proteins that circulate in the vasculature, like vitronectin.
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Affiliation(s)
- Ye Tian
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Kyungsoo Shin
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | | | - Wonpil Im
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania
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Félix Vélez NE, Gorashi RM, Aguado BA. Chemical and molecular tools to probe biological sex differences at multiple length scales. J Mater Chem B 2022; 10:7089-7098. [PMID: 36043366 PMCID: PMC9632480 DOI: 10.1039/d2tb00871h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological sex differences are observed at multiple different length scales and across organ systems. Gaps in knowledge remain regarding our understanding of how molecular, cellular, and environmental factors contribute to physiological sex differences. Here, we provide our perspective on how chemical and molecular tools can be leveraged to explore sex differences in biology at the molecular, intracellular, extracellular, tissue, and organ length scales. We provide examples where chemical and molecular tools were used to explore sex differences in the cardiovascular, nervous, immune, and reproductive systems. We also provide a future outlook where chemical and molecular tools can be applied to continue investigating sex differences in biology, with the ultimate goal of addressing inequities in biomedical research and approaches to clinical treatments.
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Affiliation(s)
- Nicole E Félix Vélez
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Rayyan M Gorashi
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Brian A Aguado
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
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Altered peripheral factors affecting the absorption, distribution, metabolism, and excretion of oral medicines in Alzheimer's disease. Adv Drug Deliv Rev 2022; 185:114282. [PMID: 35421522 DOI: 10.1016/j.addr.2022.114282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/23/2022] [Accepted: 04/06/2022] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) has traditionally been considered solely a neurological condition. Therefore, numerous studies have been conducted to identify the existence of pathophysiological changes affecting the brain and the blood-brain barrier in individuals with AD. Such studies have provided invaluable insight into possible changes to the central nervous system exposure of drugs prescribed to individuals with AD. However, there is now increasing recognition that extra-neurological systems may also be affected in AD, such as the small intestine, liver, and kidneys. Examination of these peripheral pathophysiological changes is now a burgeoning area of scientific research, owing to the potential impact of these changes on the absorption, distribution, metabolism, and excretion (ADME) of drugs used for both AD and other concomitant conditions in this population. The purpose of this review is to identify and summarise available literature reporting alterations to key organs influencing the pharmacokinetics of drugs, with any changes to the small intestine, liver, kidney, and circulatory system on the ADME of drugs described. By assessing studies in both rodent models of AD and samples from humans with AD, this review highlights possible dosage adjustment requirements for both AD and non-AD drugs so as to ensure the achievement of optimum pharmacotherapy in individuals with AD.
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8
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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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Malicek D, Wittig I, Luger S, Foerch C. Proteomics-Based Approach to Identify Novel Blood Biomarker Candidates for Differentiating Intracerebral Hemorrhage From Ischemic Stroke-A Pilot Study. Front Neurol 2022; 12:713124. [PMID: 34975707 PMCID: PMC8719589 DOI: 10.3389/fneur.2021.713124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Background: A reliable distinction between ischemic stroke (IS) and intracerebral hemorrhage (ICH) is required for diagnosis-specific treatment and effective secondary prevention in patients with stroke. However, in resource-limited settings brain imaging, which is the current diagnostic gold standard for this purpose, is not always available in time. Hence, an easily accessible and broadly applicable blood biomarker-based diagnostic test differing stroke subtypes would be desirable. Using an explorative proteomics approach, this pilot study aimed to identify novel blood biomarker candidates for distinguishing IS from ICH. Material and Methods: Plasma samples from patients with IS and ICH were drawn during hospitalization and were analyzed by using liquid chromatography/mass spectrometry. Proteins were identified using the human reference proteome database UniProtKB, and label-free quantification (LFQ) data were further analyzed using bioinformatic tools. Results: Plasma specimens of three patients with IS and four patients with ICH with a median National Institute of Health Stroke Scale (NIHSS) of 12 [interquartile range (IQR) 10.5–18.5] as well as serum samples from two healthy volunteers were analyzed. Among 495 identified protein groups, a total of 368 protein groups exhibited enough data points to be entered into quantitative analysis. Of the remaining 22 top-listed proteins, a significant difference between IS and ICH was found for Carboxypeptidase N subunit 2 (CPN2), Coagulation factor XII (FXII), Plasminogen, Mannan-binding lectin serine protease 1, Serum amyloid P-component, Paraoxonase 1, Carbonic anhydrase 1, Fibulin-1, and Granulins. Discussion: In this exploratory proteomics-based pilot study, nine candidate biomarkers for differentiation of IS and ICH were identified. The proteins belong to the immune system, the coagulation cascade, and the apoptosis system, respectively. Further investigations in larger cohorts of patients with stroke using additional biochemical analysis methods, such as ELISA or Western Blotting are now necessary to validate these markers, and to characterize diagnostic accuracy with regard to the development of a point-of-care-system for use in resource-limited areas.
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Affiliation(s)
- David Malicek
- Department of Neurology, Goethe University/University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute of Cardiovascular Physiology, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Sebastian Luger
- Department of Neurology, Goethe University/University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Christian Foerch
- Department of Neurology, Goethe University/University Hospital Frankfurt, Frankfurt am Main, Germany
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Rahman MM, Lendel C. Extracellular protein components of amyloid plaques and their roles in Alzheimer's disease pathology. Mol Neurodegener 2021; 16:59. [PMID: 34454574 PMCID: PMC8400902 DOI: 10.1186/s13024-021-00465-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 06/11/2021] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is pathologically defined by the presence of fibrillar amyloid β (Aβ) peptide in extracellular senile plaques and tau filaments in intracellular neurofibrillary tangles. Extensive research has focused on understanding the assembly mechanisms and neurotoxic effects of Aβ during the last decades but still we only have a brief understanding of the disease associated biological processes. This review highlights the many other constituents that, beside Aβ, are accumulated in the plaques, with the focus on extracellular proteins. All living organisms rely on a delicate network of protein functionality. Deposition of significant amounts of certain proteins in insoluble inclusions will unquestionably lead to disturbances in the network, which may contribute to AD and copathology. This paper provide a comprehensive overview of extracellular proteins that have been shown to interact with Aβ and a discussion of their potential roles in AD pathology. Methods that can expand the knowledge about how the proteins are incorporated in plaques are described. Top-down methods to analyze post-mortem tissue and bottom-up approaches with the potential to provide molecular insights on the organization of plaque-like particles are compared. Finally, a network analysis of Aβ-interacting partners with enriched functional and structural key words is presented.
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Affiliation(s)
- M Mahafuzur Rahman
- Department of Chemistry, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden.
| | - Christofer Lendel
- Department of Chemistry, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden.
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11
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Khan MJ, Desaire H, Lopez OL, Kamboh MI, Robinson RA. Why Inclusion Matters for Alzheimer's Disease Biomarker Discovery in Plasma. J Alzheimers Dis 2021; 79:1327-1344. [PMID: 33427747 PMCID: PMC9126484 DOI: 10.3233/jad-201318] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND African American/Black adults have a disproportionate incidence of Alzheimer's disease (AD) and are underrepresented in biomarker discovery efforts. OBJECTIVE This study aimed to identify potential diagnostic biomarkers for AD using a combination of proteomics and machine learning approaches in a cohort that included African American/Black adults. METHODS We conducted a discovery-based plasma proteomics study on plasma samples (N = 113) obtained from clinically diagnosed AD and cognitively normal adults that were self-reported African American/Black or non-Hispanic White. Sets of differentially-expressed proteins were then classified using a support vector machine (SVM) to identify biomarker candidates. RESULTS In total, 740 proteins were identified of which, 25 differentially-expressed proteins in AD came from comparisons within a single racial and ethnic background group. Six proteins were differentially-expressed in AD regardless of racial and ethnic background. Supervised classification by SVM yielded an area under the curve (AUC) of 0.91 and accuracy of 86%for differentiating AD in samples from non-Hispanic White adults when trained with differentially-expressed proteins unique to that group. However, the same model yielded an AUC of 0.49 and accuracy of 47%for differentiating AD in samples from African American/Black adults. Other covariates such as age, APOE4 status, sex, and years of education were found to improve the model mostly in the samples from non-Hispanic White adults for classifying AD. CONCLUSION These results demonstrate the importance of study designs in AD biomarker discovery, which must include diverse racial and ethnic groups such as African American/Black adults to develop effective biomarkers.
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Affiliation(s)
- Mostafa J. Khan
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS, USA
| | - Oscar L. Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - M. Ilyas Kamboh
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A.S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
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12
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Maher D, Ailabouni N, Mangoni AA, Wiese MD, Reeve E. Alterations in drug disposition in older adults: a focus on geriatric syndromes. Expert Opin Drug Metab Toxicol 2020; 17:41-52. [PMID: 33078628 DOI: 10.1080/17425255.2021.1839413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Age-associated physiological changes can alter the disposition of drugs, however, pathophysiological changes associated with geriatric syndromes in older adults may lead to even greater heterogeneity in pharmacokinetics. Geriatric syndromes are common health problems in older adults which have multifactorial causes and do not fit into distinct organ-based disease categories. With older adults being the greatest users of medications, understanding both age- and geriatric syndrome-related changes is important clinically to ensure safe and effective medication use. AREAS COVERED This review provides an overview of current evidence regarding pharmacokinetic alterations that occur with aging and in common geriatric syndromes, including frailty, sarcopenia, dementia, polypharmacy and enteral feeding. The evidence is presented according to the four primary pharmacokinetic processes (Absorption, Distribution, Metabolism and Excretion). EXPERT OPINION There is some evidence to inform our understanding of the impact of chronological aging and various geriatric syndromes on drug disposition. However, many areas require more research, including drug induced inhibition and induction of cytochrome P450 enzymes and the clinical utility of emerging methods for estimating renal function. There is a need to develop tools to predict alterations in drug disposition in subgroups of older adults, particularly where the currently available clinical information is sparse.
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Affiliation(s)
- Dorsa Maher
- Health and Biomedical Innovation, UniSA: Clinical and Health Sciences, University of South Australia , Adelaide, Australia
| | - Nagham Ailabouni
- Quality Use of Medicines and Pharmacy Research Centre, UniSA: Clinical and Health Sciences, University of South Australia , Australia
| | - Arduino A Mangoni
- Department of Clinical Pharmacology, Flinders University and Flinders Medical Centre , Bedford Park, Australia
| | - Michael D Wiese
- Health and Biomedical Innovation, UniSA: Clinical and Health Sciences, University of South Australia , Adelaide, Australia
| | - Emily Reeve
- Quality Use of Medicines and Pharmacy Research Centre, UniSA: Clinical and Health Sciences, University of South Australia , Australia.,Geriatric Medicine Research, Faculty of Medicine, and College of Pharmacy, Dalhousie University and Nova Scotia Health Authority , Halifax, Canada
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13
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Bai S, Chaurasiya AH, Banarjee R, Walke PB, Rashid F, Unnikrishnan AG, Kulkarni MJ. CD44, a Predominant Protein in Methylglyoxal-Induced Secretome of Muscle Cells, is Elevated in Diabetic Plasma. ACS OMEGA 2020; 5:25016-25028. [PMID: 33043179 PMCID: PMC7542587 DOI: 10.1021/acsomega.0c01318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Methylglyoxal (MG), a glycolytic intermediate and reactive dicarbonyl, is responsible for exacerbation of insulin resistance and diabetic complication. In this study, MG-induced secretome of rat muscle cells was identified and relatively quantified by SWATH-MS. A total of 643 proteins were identified in MG-induced secretome, of which 82 proteins were upregulated and 99 proteins were downregulated by more than 1.3-fold in SWATH analysis. Further, secretory proteins from the classical secretory pathway and nonclassical secretory pathway were identified using SignalP and SecretomeP, respectively. A total of 180 proteins were identified with SignalP, and 113 proteins were identified with SecretomeP. The differentially expressed proteins were functionally annotated by KEGG pathway analysis using Cytoscape software with plugin clusterMaker. The differentially expressed proteins were found to be involved in various pathways like extracellular matrix (ECM)-receptor interaction, leukocyte transendothelial migration, fluid shear stress and atherosclerosis, complement and coagulation cascades, and lysosomal pathway. Since the MG levels are high in diabetic conditions, the presence of MG-induced secreted proteins was inspected by profiling human plasma of healthy and diabetic subjects (n = 10 each). CD44, a predominant MG-induced secreted protein, was found to be elevated in the diabetic plasma and to have a role in the development of insulin resistance.
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Affiliation(s)
- Shakuntala Bai
- Proteomics
Facility, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Arvindkumar H. Chaurasiya
- Proteomics
Facility, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Reema Banarjee
- Proteomics
Facility, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Prachi B. Walke
- Proteomics
Facility, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Faraz Rashid
- Sciex, 121 DHR, Udyog Vihar, Phase IV, Gurugram 122015, Haryana, India
| | | | - Mahesh J. Kulkarni
- Proteomics
Facility, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
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14
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Xu J, Bankov G, Kim M, Wretlind A, Lord J, Green R, Hodges A, Hye A, Aarsland D, Velayudhan L, Dobson RJB, Proitsi P, Legido-Quigley C. Integrated lipidomics and proteomics network analysis highlights lipid and immunity pathways associated with Alzheimer's disease. Transl Neurodegener 2020; 9:36. [PMID: 32951606 PMCID: PMC7504646 DOI: 10.1186/s40035-020-00215-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/18/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND There is an urgent need to understand the pathways and processes underlying Alzheimer's disease (AD) for early diagnosis and development of effective treatments. This study was aimed to investigate Alzheimer's dementia using an unsupervised lipid, protein and gene multi-omics integrative approach. METHODS A lipidomics dataset comprising 185 AD patients, 40 mild cognitive impairment (MCI) individuals and 185 controls, and two proteomics datasets (295 AD, 159 MCI and 197 controls) were used for weighted gene co-expression network analyses (WGCNA). Correlations of modules created within each modality with clinical AD diagnosis, brain atrophy measures and disease progression, as well as their correlations with each other, were analyzed. Gene ontology enrichment analysis was employed to examine the biological processes and molecular and cellular functions of protein modules associated with AD phenotypes. Lipid species were annotated in the lipid modules associated with AD phenotypes. The associations between established AD risk loci and the lipid/protein modules that showed high correlation with AD phenotypes were also explored. RESULTS Five of the 20 identified lipid modules and five of the 17 identified protein modules were correlated with clinical AD diagnosis, brain atrophy measures and disease progression. The lipid modules comprising phospholipids, triglycerides, sphingolipids and cholesterol esters were correlated with AD risk loci involved in immune response and lipid metabolism. The five protein modules involved in positive regulation of cytokine production, neutrophil-mediated immunity, and humoral immune responses were correlated with AD risk loci involved in immune and complement systems and in lipid metabolism (the APOE ε4 genotype). CONCLUSIONS Modules of tightly regulated lipids and proteins, drivers in lipid homeostasis and innate immunity, are strongly associated with AD phenotypes.
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Affiliation(s)
- Jin Xu
- Institute of Pharmaceutical Science, King's College London, London, UK
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Giulia Bankov
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Min Kim
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | | | - Jodie Lord
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Rebecca Green
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Angela Hodges
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Abdul Hye
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Dag Aarsland
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Center for Age-Related Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Latha Velayudhan
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Richard J B Dobson
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
| | - Petroula Proitsi
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
| | - Cristina Legido-Quigley
- Institute of Pharmaceutical Science, King's College London, London, UK.
- Steno Diabetes Center Copenhagen, Gentofte, Denmark.
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15
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Dufresne J, Bowden P, Thavarajah T, Florentinus-Mefailoski A, Chen ZZ, Tucholska M, Norzin T, Ho MT, Phan M, Mohamed N, Ravandi A, Stanton E, Slutsky AS, Dos Santos CC, Romaschin A, Marshall JC, Addison C, Malone S, Heyland D, Scheltens P, Killestein J, Teunissen C, Diamandis EP, Siu KWM, Marshall JG. The plasma peptides of breast versus ovarian cancer. Clin Proteomics 2019; 16:43. [PMID: 31889940 PMCID: PMC6927194 DOI: 10.1186/s12014-019-9262-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Background There is a need to demonstrate a proof of principle that proteomics has the capacity to analyze plasma from breast cancer versus other diseases and controls in a multisite clinical trial design. The peptides or proteins that show a high observation frequency, and/or precursor intensity, specific to breast cancer plasma might be discovered by comparison to other diseases and matched controls. The endogenous tryptic peptides of breast cancer plasma were compared to ovarian cancer, female normal, sepsis, heart attack, Alzheimer's and multiple sclerosis along with the institution-matched normal and control samples collected directly onto ice. Methods Endogenous tryptic peptides were extracted from individual breast cancer and control EDTA plasma samples in a step gradient of acetonitrile, and collected over preparative C18 for LC-ESI-MS/MS with a set of LTQ XL linear quadrupole ion traps working together in parallel to randomly and independently sample clinical populations. The MS/MS spectra were fit to fully tryptic peptides or phosphopeptides within proteins using the X!TANDEM algorithm. The protein observation frequency was counted using the SEQUEST algorithm after selecting the single best charge state and peptide sequence for each MS/MS spectra. The observation frequency was subsequently tested by Chi Square analysis. The log10 precursor intensity was compared by ANOVA in the R statistical system. Results Peptides and/or phosphopeptides of common plasma proteins such as APOE, C4A, C4B, C3, APOA1, APOC2, APOC4, ITIH3 and ITIH4 showed increased observation frequency and/or precursor intensity in breast cancer. Many cellular proteins also showed large changes in frequency by Chi Square (χ2 > 100, p < 0.0001) in the breast cancer samples such as CPEB1, LTBP4, HIF-1A, IGHE, RAB44, NEFM, C19orf82, SLC35B1, 1D12A, C8orf34, HIF1A, OCLN, EYA1, HLA-DRB1, LARS, PTPDC1, WWC1, ZNF562, PTMA, MGAT1, NDUFA1, NOGOC, OR1E1, OR1E2, CFI, HSA12, GCSH, ELTD1, TBX15, NR2C2, FLJ00045, PDLIM1, GALNT9, ASH2L, PPFIBP1, LRRC4B, SLCO3A1, BHMT2, CS, FAM188B2, LGALS7, SAT2, SFRS8, SLC22A12, WNT9B, SLC2A4, ZNF101, WT1, CCDC47, ERLIN1, SPFH1, EID2, THOC1, DDX47, MREG, PTPRE, EMILIN1, DKFZp779G1236 and MAP3K8 among others. The protein gene symbols with large Chi Square values were significantly enriched in proteins that showed a complex set of previously established functional and structural relationships by STRING analysis. An increase in mean precursor intensity of peptides was observed for QSER1 as well as SLC35B1, IQCJ-SCHIP1, MREG, BHMT2, LGALS7, THOC1, ANXA4, DHDDS, SAT2, PTMA and FYCO1 among others. In contrast, the QSER1 peptide QPKVKAEPPPK was apparently specific to ovarian cancer. Conclusion There was striking agreement between the breast cancer plasma peptides and proteins discovered by LC-ESI-MS/MS with previous biomarkers from tumors, cells lines or body fluids by genetic or biochemical methods. The results indicate that variation in plasma peptides from breast cancer versus ovarian cancer may be directly discovered by LC-ESI-MS/MS that will be a powerful tool for clinical research. It may be possible to use a battery of sensitive and robust linear quadrupole ion traps for random and independent sampling of plasma from a multisite clinical trial.
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Affiliation(s)
- Jaimie Dufresne
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Pete Bowden
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Thanusi Thavarajah
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Angelique Florentinus-Mefailoski
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Zhuo Zhen Chen
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Monika Tucholska
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Tenzin Norzin
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Margaret Truc Ho
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Morla Phan
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Nargiz Mohamed
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Amir Ravandi
- 2Institute of Cardiovascular Sciences, St. Boniface Hospital Research Center, University of Manitoba, Winnipeg, Canada
| | - Eric Stanton
- 3Division of Cardiology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Arthur S Slutsky
- 4St. Michael's Hospital, Keenan Chair in Medicine, Professor of Medicine, Surgery & Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Claudia C Dos Santos
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Alexander Romaschin
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - John C Marshall
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Christina Addison
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Shawn Malone
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Daren Heyland
- 7Clinical Evaluation Research Unit, Kingston General Hospital, Kingston, Canada
| | - Philip Scheltens
- 8Alzheimer Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Joep Killestein
- 9MS Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Charlotte Teunissen
- 10Neurochemistry Lab and Biobank, Dept of Clinical Chemsitry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | | | - K W M Siu
- 12University of Windsor, Windsor, Canada
| | - John G Marshall
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada.,13International Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (formerly CRP Sante Luxembourg), Strassen, Luxembourg
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16
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Eke CS, Jammeh E, Li X, Carroll C, Pearson S, Ifeachor E. Identification of Optimum Panel of Blood-based Biomarkers for Alzheimer's Disease Diagnosis Using Machine Learning. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2019; 2018:3991-3994. [PMID: 30441233 DOI: 10.1109/embc.2018.8513293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
With the increasing number of people living with Alzheimer's disease (AD), there is a need for low-cost and easy to use methods to detect AD early to facilitate access to appropriate care pathways. Neuroimaging biomarkers (such as those based on PET and MRI) and biochemical biomarkers (such as those based on CSF) are recommended by international guidelines to facilitate diagnosis. However, neuroimaging is expensive and may not be widely available and CSF testing is invasive. Bloodbased biomarkers offer the potential for the development of a low-cost and more time efficient tool to detect AD to complement CSF and neuroimaging as blood is much easier to obtain. Although no single blood biomarker is yet able to detect AD, combinations of biomarkers (also called panels) have shown good results. However, a large number of biomarkers are often needed to achieve a satisfactory detection performance. In addition, it is difficult to reproduce reported results within and across different study cohorts because of data overfitting and lack of access to the datasets used in the studies. In this study, our focus is to identify an optimum panel (in terms of the least number of blood biomarkers to meet the specified diagnostic performance of 80% sensitivity and specificity) based on a widely accessible data set, and to demonstrate a testing methodology that reinforces reproducibility of results. Realizing a panel with reduced number of markers will have significant impact on the complexity and cost of diagnosis and potential development of cost-effective point of care devices.
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17
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Xu N, Li AD, Ji LL, Ye Y, Wang ZY, Tong L. miR-132 regulates the expression of synaptic proteins in APP/PS1 transgenic mice through C1q. Eur J Histochem 2019; 63. [PMID: 31060348 PMCID: PMC6511887 DOI: 10.4081/ejh.2019.3008] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/01/2019] [Indexed: 02/02/2023] Open
Abstract
Cognitive impairment in Alzheimer’s disease (AD) is usually accompanied by synaptic loss in both the hippocampus and neocortex. In the early stage of AD, amyloid β-induced synapse changes is the main reason, while in the later stage, the accumulation of Tau protein promotes synapse degeneration as the key factor leading to dementia. MicroRNA (miRNA) is closely related to the expression changes of many AD-related genes. One of the most abundant brain-enriched miRNAs is miR-132, which has been shown to regulate both neuron morphogenesis and plasticity. It has been reported that miR-132 is significantly reduced in the brains of Alzheimer’s patients. Genetic deletion of miR-132 in mice promotes Aβ deposition, leading to impaired memory and enhanced Tau pathology, but how the miRNA-mediated gene expression dysregulation contributes to AD pathology remains unclear. Here we found the possible downstream target of miR-132 by in silico analysis, namely C1q. C1q is the primary protein of classical complement cascade, which is highly expressed in the synaptic regions of the central nervous system in Alzheimer’s patients. However, it is not clear whether miR-132 plays a role in AD through regulating C1q. To address this question, the APP/PS1 transgenic mice were transfected with miR-132 and given C1 inhibitors. Behavior tests were conducted to assess memory and cognitive abilities seven days after administration. In addition, we analyzed the expression of PSD95, Synapsin-1 and phosphorylated (p)- Synapsin. We found that the expression levels of the synaptic proteins treated with miR-132 or C1INH were significantly increased compared with the AD group. Further RT-qPCR result suggested that miR-132 might regulate C1q expression in AD.
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Affiliation(s)
- Nan Xu
- Department of Anatomy, College of Basic Medical Sciences, China Medical University, Shenyang.
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18
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Dufresne J, Bowden P, Thavarajah T, Florentinus-Mefailoski A, Chen ZZ, Tucholska M, Norzin T, Ho MT, Phan M, Mohamed N, Ravandi A, Stanton E, Slutsky AS, Dos Santos CC, Romaschin A, Marshall JC, Addison C, Malone S, Heyland D, Scheltens P, Killestein J, Teunissen CE, Diamandis EP, Michael Siu KW, Marshall JG. The plasma peptides of ovarian cancer. Clin Proteomics 2018; 15:41. [PMID: 30598658 PMCID: PMC6302491 DOI: 10.1186/s12014-018-9215-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/19/2018] [Indexed: 12/13/2022] Open
Abstract
Background It may be possible to discover new diagnostic or therapeutic peptides or proteins from blood plasma by using liquid chromatography and tandem mass spectrometry to identify, quantify and compare the peptides cleaved ex vivo from different clinical populations. The endogenous tryptic peptides of ovarian cancer plasma were compared to breast cancer and female cancer normal controls, other diseases with their matched or normal controls, plus ice cold plasma to control for pre-analytical variation. Methods The endogenous tryptic peptides or tryptic phospho peptides (i.e. without exogenous digestion) were analyzed from 200 μl of EDTA plasma. The plasma peptides were extracted by a step gradient of organic/water with differential centrifugation, dried, and collected over C18 for analytical HPLC nano electrospray ionization and tandem mass spectrometry (LC–ESI–MS/MS) with a linear quadrupole ion trap. The endogenous peptides of ovarian cancer were compared to multiple disease and normal samples from different institutions alongside ice cold controls. Peptides were randomly and independently sampled by LC–ESI–MS/MS. Precursor ions from peptides > E4 counts were identified by the SEQUEST and X!TANDEM algorithms, filtered in SQL Server, before testing of frequency counts by Chi Square (χ2), for analysis with the STRING algorithm, and comparison of precursor intensity by ANOVA in the R statistical system with the Tukey-Kramer Honestly Significant Difference (HSD) test. Results Peptides and/or phosphopeptides of common plasma proteins such as HPR, HP, HPX, and SERPINA1 showed increased observation frequency and/or precursor intensity in ovarian cancer. Many cellular proteins showed large changes in frequency by Chi Square (χ2 > 60, p < 0.0001) in the ovarian cancer samples such as ZNF91, ZNF254, F13A1, LOC102723511, ZNF253, QSER1, P4HA1, GPC6, LMNB2, PYGB, NBR1, CCNI2, LOC101930455, TRPM5, IGSF1, ITGB1, CHD6, SIRT1, NEFM, SKOR2, SUPT20HL1, PLCE1, CCDC148, CPSF3, MORN3, NMI, XTP11, LOC101927572, SMC5, SEMA6B, LOXL3, SEZ6L2, and DHCR24. The protein gene symbols with large Chi Square values were significantly enriched in proteins that showed a complex set of previously established functional and structural relationships by STRING analysis. Analysis of the frequently observed proteins by ANOVA confirmed increases in mean precursor intensity in ZFN91, TRPM5, SIRT1, CHD6, RIMS1, LOC101930455 (XP_005275896), CCDC37 and GIMAP4 between ovarian cancer versus normal female and other diseases or controls by the Tukey–Kramer HSD test. Conclusion Here we show that separation of endogenous peptides with a step gradient of organic/water and differential centrifugation followed by random and independent sampling by LC–ESI–MS/MS with analysis of peptide frequency and intensity by SQL Server and R revealed significant difference in the ex vivo cleavage of peptides between ovarian cancer and other clinical treatments. There was striking agreement between the proteins discovered from cancer plasma versus previous biomarkers discovered in tumors by genetic or biochemical methods. The results indicate that variation in plasma proteins from ovarian cancer may be directly discovered by LC–ESI–MS/MS that will be a powerful tool for clinical research. Electronic supplementary material The online version of this article (10.1186/s12014-018-9215-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaimie Dufresne
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Pete Bowden
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Thanusi Thavarajah
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | | | - Zhuo Zhen Chen
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Monika Tucholska
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Tenzin Norzin
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Margaret Truc Ho
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Morla Phan
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Nargiz Mohamed
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Amir Ravandi
- 2Institute of Cardiovascular Sciences, St Boniface Hospital Research Center, University of Manitoba, Winnipeg, Canada
| | - Eric Stanton
- 3Division of Cardiology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Arthur S Slutsky
- 4Keenan Chair in Medicine, St. Michael's Hospital, University of Toronto, Toronto, Canada
| | - Claudia C Dos Santos
- 5Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada
| | - Alexander Romaschin
- 5Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada
| | - John C Marshall
- 5Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada
| | - Christina Addison
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Shawn Malone
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Daren Heyland
- 7Clinical Evaluation Research Unit, Kingston General Hospital, Kingston, Canada
| | - Philip Scheltens
- 8Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, The Netherlands
| | - Joep Killestein
- 9MS Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- 10Neurochemistry Lab and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - John G Marshall
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada.,13International Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (formerly CRP Sante Luxembourg), Strassen, Luxembourg.,14Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
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19
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Sohail W, Majeed F, Afroz A. Differential proteome analysis of diabetes mellitus type 2 and its pathophysiological complications. Diabetes Metab Syndr 2018; 12:1125-1131. [PMID: 29907545 DOI: 10.1016/j.dsx.2018.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 06/05/2018] [Indexed: 01/18/2023]
Abstract
The prevalence of Diabetes Mellitus Type 2 (DM 2) is increasing every passing year due to some global changes in lifestyles of people. The exact underlying mechanisms of the progression of this disease are not yet known. However recent advances in the combined omics more particularly in proteomics and genomics have opened a gateway towards the understanding of predetermined genetic factors, progression, complications and treatment of this disease. Here we shall review the recent advances in proteomics that have led to an early and better diagnostic approaches in controlling DM 2 more importantly the comparison of structural and functional protein biomarkers that are modified in the diseased state. By applying these advanced and promising proteomic strategies with bioinformatics applications and bio-statistical tools the prevalence of DM 2 and its associated disorders i-e nephropathy and retinopathy are expected to be controlled.
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Affiliation(s)
- Waleed Sohail
- Department of Biochemistry and Molecular Biology, University of Gujrat, Pakistan.
| | - Fatimah Majeed
- Department of Biochemistry and Molecular Biology, University of Gujrat, Pakistan
| | - Amber Afroz
- Department of Biochemistry and Molecular Biology, University of Gujrat, Pakistan
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20
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Pereira-Fantini PM, Byars SG, McCall KE, Perkins EJ, Oakley RB, Dellacà RL, Dargaville PA, Davis PG, Ignjatovic V, Tingay DG. Plasma proteomics reveals gestational age-specific responses to mechanical ventilation and identifies the mechanistic pathways that initiate preterm lung injury. Sci Rep 2018; 8:12616. [PMID: 30135517 PMCID: PMC6105628 DOI: 10.1038/s41598-018-30868-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/02/2018] [Indexed: 12/15/2022] Open
Abstract
The preterm lung is particularly vulnerable to ventilator-induced lung injury (VILI) as a result of mechanical ventilation. However the developmental and pathological cellular mechanisms influencing the changing patterns of VILI have not been comprehensively delineated, preventing the advancement of targeted lung protective therapies. This study aimed to use SWATH-MS to comprehensively map the plasma proteome alterations associated with the initiation of VILI following 60 minutes of standardized mechanical ventilation from birth in three distinctly different developmental lung states; the extremely preterm, preterm and term lung using the ventilated lamb model. Across these gestations, 34 proteins were differentially altered in matched plasma samples taken at birth and 60 minutes. Multivariate analysis of the plasma proteomes confirmed a gestation-specific response to mechanical ventilation with 79% of differentially-expressed proteins altered in a single gestation group only. Six cellular and molecular functions and two physiological functions were uniquely enriched in either the extremely preterm or preterm group. Correlation analysis supported gestation-specific protein-function associations within each group. In identifying the gestation-specific proteome and functional responses to ventilation we provide the founding evidence required for the potential development of individualized respiratory support approaches tailored to both the developmental and pathological state of the lung.
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Affiliation(s)
- Prue M Pereira-Fantini
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia. .,Department of Paediatrics, University of Melbourne, Parkville, Australia.
| | - Sean G Byars
- Department of Pathology, University of Melbourne, Parkville, Australia.,Centre for Systems Genomics, University of Melbourne, Parkville, Australia
| | - Karen E McCall
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia.,University College Dublin, Dublin, Ireland
| | - Elizabeth J Perkins
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia
| | - Regina B Oakley
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia
| | - R L Dellacà
- Laboratorio di Tecnologie Biomediche, Dipartimento di Elettronica, Informazione e Ingegneria Biomedica-DEIB, Politecnico di Milano University, Milano, Italy
| | - Peter A Dargaville
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Peter G Davis
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia.,The Royal Women's Hospital, Parkville, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Australia
| | - Vera Ignjatovic
- Department of Paediatrics, University of Melbourne, Parkville, Australia.,Haematology Research, Murdoch Childrens Research Institute, Parkville, Australia
| | - David G Tingay
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,Department of Neonatology, Royal Children's Hospital, Parkville, Australia
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21
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Dufresne J, Florentinus-Mefailoski A, Bowden P, Marshall JG. A method for the extraction of the endogenous tryptic peptides (peptidome) from human EDTA plasma. Anal Biochem 2018; 549:188-196. [PMID: 29486203 DOI: 10.1016/j.ab.2018.02.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 10/18/2022]
Abstract
The proteins identified from endogenous peptides agreed between serum versus plasma, and tryptic versus non-tryptic peptides, when collected by C18 alone and analyzed by liquid chromatography electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) including amyloids, apolipoproteins, haptoglobin, complements, fibrinogens, hemopexin, antitrypsin and alpha 2 macroglobulin. Precipitation of polypeptides from plasma in 9 vol of 100% organic solvent followed by stepwise extraction of the insoluble pellet with an increasing fraction of water identified thousands of proteins. A Coomassie-blue protein binding assay, and tricine SDS-PAGE, showed that Acetonitrile-Water (AH) resulted in a greater relative enrichment of low molecular weight plasma polypeptides than Acetonitrile-Methanol Water (AMH). A total of 905,386 MS/MS spectra greater than ~10,000 (E4) counts were correlated by X!TANDEM to a federated human protein library of 153,124 different protein sequences that resulted in 58,223 fully tryptic peptides from 3463 Gene Symbols of which 1880 had ≥ 5 independent peptides (p ≤ 0.00001). The results were filtered and organized in an SQL database for analysis using the generic R statistical analysis system. Cellular proteins including secreted and exosome proteins, signaling factors, nucleic acid binding proteins, metabolic enzymes and uncharacterized factors were observed with a significant enrichment of expected protein-protein interactions by STRING analysis.
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Affiliation(s)
- Jaimie Dufresne
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, Toronto, ON, M5B 2K3, Canada
| | - Angelique Florentinus-Mefailoski
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, Toronto, ON, M5B 2K3, Canada
| | - Pete Bowden
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, Toronto, ON, M5B 2K3, Canada
| | - John G Marshall
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, Toronto, ON, M5B 2K3, Canada.
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22
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Shen L, Liao L, Chen C, Guo Y, Song D, Wang Y, Chen Y, Zhang K, Ying M, Li S, Liu Q, Ni J. Proteomics Analysis of Blood Serums from Alzheimer's Disease Patients Using iTRAQ Labeling Technology. J Alzheimers Dis 2018; 56:361-378. [PMID: 27911324 DOI: 10.3233/jad-160913] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alzheimer' disease (AD) is the most common form of dementia affecting up to 6% of the population over the age of 65. In order to discover differentially expressed proteins that might serve as potential biomarkers, the serums from AD patients and healthy controls were compared and analyzed using the proteomics approach of isobaric tagging for relative and absolute quantitation (iTRAQ). For the first time, AD biomarkers in serums are investigated in the Han Chinese population using iTRAQ labeled proteomics strategy. Twenty-two differentially expressed proteins were identified and out of which nine proteins were further validated with more sample test. Another three proteins that have been reported in the literature to be potentially associated with AD were also investigated for alteration in expression level. Functions of those proteins were mainly related to the following processes: amyloid-β (Aβ) metabolism, cholesterol transport, complement and coagulation cascades, immune response, inflammation, hemostasis, hyaluronan metabolism, and oxidative stress. These results support current views on the molecular mechanism of AD. For the first time, differential expression of zinc-alpha-2-glycoprotein (AZGP1), fibulin-1 (FBLN1), platelet basic protein (PPBP), thrombospondin-1 (THBS1), S100 calcium-binding protein A8 (S100A8), and S100 calcium-binding protein A9 (S100A9) were detected in the serums of AD patients compared with healthy controls. These proteins might play a role in AD pathophysiology and serve as potential biomarkers for AD diagnosis. Specifically, our results strengthened the crucial role of Aβ metabolism and blood coagulation in AD pathogenesis and proteins related to these two processes may be used as peripheral blood biomarkers for AD.
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Affiliation(s)
- Liming Shen
- College of Life Science and Oceanography, Shenzhen Key Laboratory of Marine Biotechnology and Ecology, Shenzhen University, Shenzhen, P.R. China
| | - Liping Liao
- College of Life Science and Oceanography, Shenzhen Key Laboratory of Marine Biotechnology and Ecology, Shenzhen University, Shenzhen, P.R. China
| | - Cheng Chen
- College of Life Science and Oceanography, Shenzhen Key Laboratory of Marine Biotechnology and Ecology, Shenzhen University, Shenzhen, P.R. China
| | - Yi Guo
- Department of Neurology, Shenzhen People's Hospital, P.R. China
| | - Dalin Song
- Department of Geriatrics, Qingdao Municipal Hospital, Qingdao, P.R. China
| | - Yong Wang
- College of Life Science and Oceanography, Shenzhen Key Laboratory of Marine Biotechnology and Ecology, Shenzhen University, Shenzhen, P.R. China
| | - Youjiao Chen
- College of Life Science and Oceanography, Shenzhen Key Laboratory of Marine Biotechnology and Ecology, Shenzhen University, Shenzhen, P.R. China
| | - Kaoyuan Zhang
- College of Life Science and Oceanography, Shenzhen Key Laboratory of Marine Biotechnology and Ecology, Shenzhen University, Shenzhen, P.R. China
| | - Ming Ying
- College of Life Science and Oceanography, Shenzhen Key Laboratory of Marine Biotechnology and Ecology, Shenzhen University, Shenzhen, P.R. China
| | - Shuiming Li
- College of Life Science and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, P.R. China
| | - Qiong Liu
- College of Life Science and Oceanography, Shenzhen Key Laboratory of Marine Biotechnology and Ecology, Shenzhen University, Shenzhen, P.R. China
| | - Jiazuan Ni
- College of Life Science and Oceanography, Shenzhen Key Laboratory of Marine Biotechnology and Ecology, Shenzhen University, Shenzhen, P.R. China
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23
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Zhu CJ, Jiang GX, Chen JM, Zhou ZM, Cheng Q. Serum haptoglobin in Chinese patients with Alzheimer's disease and mild cognitive impairment: A case-control study. Brain Res Bull 2018; 137:301-305. [PMID: 29325993 DOI: 10.1016/j.brainresbull.2018.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/28/2017] [Accepted: 01/04/2018] [Indexed: 01/21/2023]
Abstract
BACKGROUND Serum level of Haptoglobin (Hp) maybe associated with Alzheimer's disease (AD) and mild cognitive impairment (MCI). OBJECTIVE To investigate associations between serum Hp and AD, as well as between Hp and MCI. METHODS Serum levels of Hp were measured and analyzed for 51 patients with AD, 139 patients with MCI and their healthy controls matched with sex and age. All study subjects were from a survey among residents aged 60 years and over in a community located in the southwest suburb of Shanghai. RESULTS Serum levels of Hp were observed significantly higher in AD and MCI cases than controls (both p < 0.0001). A significant positive correlation was found between Hp and Activities of Daily Living (ADL) score (rs = 0.430, p = 0.007), as well as between Hp and Clinical Dementia Rating (CDR) score (rs = 0.359, p = 0.027) in all AD patients. According to the receiver operating characteristic (ROC) curve analysis, the optimal cut-off point for Hp was found to be 67.50 μg/ml (sensitivity, 0.902; specificity, 0.745) in AD patients, and 44.76 μg/ml (sensitivity, 0.986; specificity, 0.403) in MCI patients. CONCLUSION Elevated serum levels of Hp were observed in AD and MCI patients than controls. In addition, Hp may correlate with the severity of AD.
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Affiliation(s)
- Cen-Jing Zhu
- Department of Neurology, Ruijin Hospital affiliated with the School of Medicine, Shanghai Jiao Tong University, 197 Ruijin No. 2 Road, Shanghai, 200025, China; School of Public Health, Shanghai Jiao Tong University, 227 Chong Qing Nan Road, Shanghai, 200025, China
| | - Guo-Xin Jiang
- Department of Learning, Informatics, Management and Ethics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Jin-Mei Chen
- Department of Neurology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 280 Mo He Road, Shanghai, 201999,China
| | - Zhi-Ming Zhou
- Sheshan Town Community Health Service Center in Shanghai, 11 Xi Lin Road, Shanghai, 201602, China
| | - Qi Cheng
- Department of Neurology, Ruijin Hospital affiliated with the School of Medicine, Shanghai Jiao Tong University, 197 Ruijin No. 2 Road, Shanghai, 200025, China; School of Public Health, Shanghai Jiao Tong University, 227 Chong Qing Nan Road, Shanghai, 200025, China.
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24
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Zhao B, Serrano MAC, Gao J, Zhuang J, Vachet RW, Thayumanavan S. Self-assembly of random co-polymers for selective binding and detection of peptides. Polym Chem 2017; 9:1066-1071. [PMID: 29725358 DOI: 10.1039/c7py01947e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Amphiphilic random co-polymers, which form stable reverse micelle-type assemblies, have been designed and synthesized. We demonstrate that the reverse micelles, formed by these co-polymers are capable of selectively binding peptides through electrostatic interactions, indicating that these random polymers can self-organize into functionally selective materials. Moreover, these random co-polymers also enable the ordered co-crystallization of matrix and extracted guest molecules, giving rise to substantial signal enhancements during MALDI-MS detection. Together, these observations represent an excellent example of how random polymers can self-assemble into ordered, functional materials.
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Affiliation(s)
- Bo Zhao
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Mahalia A C Serrano
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Jingjing Gao
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Jiaming Zhuang
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.,Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003, USA.,Center for Bioactive Delivery- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - S Thayumanavan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.,Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003, USA.,Center for Bioactive Delivery- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
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25
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Dufresne J, Florentinus-Mefailoski A, Ajambo J, Ferwa A, Bowden P, Marshall J. Random and independent sampling of endogenous tryptic peptides from normal human EDTA plasma by liquid chromatography micro electrospray ionization and tandem mass spectrometry. Clin Proteomics 2017; 14:41. [PMID: 29234243 PMCID: PMC5721679 DOI: 10.1186/s12014-017-9176-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/26/2017] [Indexed: 12/12/2022] Open
Abstract
Background Normal human EDTA plasma samples were collected on ice, processed ice cold, and stored in a freezer at – 80 °C prior to experiments. Plasma test samples from the – 80 °C freezer were thawed on ice or intentionally warmed to room temperature. Methods Protein content was measured by CBBR binding and the release of alcohol soluble amines by the Cd ninhydrin assay. Plasma peptides released over time were collected over C18 for random and independent sampling by liquid chromatography micro electrospray ionization and tandem mass spectrometry (LC–ESI–MS/MS) and correlated with X!TANDEM. Results Fully tryptic peptides by X!TANDEM returned a similar set of proteins, but was more computationally efficient, than “no enzyme” correlations. Plasma samples maintained on ice, or ice with a cocktail of protease inhibitors, showed lower background amounts of plasma peptides compared to samples incubated at room temperature. Regression analysis indicated that warming plasma to room temperature, versus ice cold, resulted in a ~ twofold increase in the frequency of peptide identification over hours–days of incubation at room temperature. The type I error rate of the protein identification from the X!TANDEM algorithm combined was estimated to be low compared to a null model of computer generated random MS/MS spectra. Conclusion The peptides of human plasma were identified and quantified with low error rates by random and independent sampling that revealed 1000s of peptides from hundreds of human plasma proteins from endogenous tryptic peptides. Electronic supplementary material The online version of this article (10.1186/s12014-017-9176-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaimie Dufresne
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | | | - Juliet Ajambo
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - Ammara Ferwa
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - Peter Bowden
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - John Marshall
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada.,Integrated BioBank of Luxembourg, 6 r. Nicolas-Ernest Barblé, Dudelange, 1210 Luxembourg
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26
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Ke M, Wu H, Zhu Z, Zhang C, Zhang Y, Deng Y. Differential proteomic analysis of white adipose tissues from T2D KKAy mice by LC-ESI-QTOF. Proteomics 2017; 17. [PMID: 27995753 DOI: 10.1002/pmic.201600219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 11/28/2016] [Accepted: 12/13/2016] [Indexed: 12/14/2022]
Abstract
Type 2 diabetes (T2D) has become a worldwide increasingly social health burden for its high morbidity and heightened prevalence. As one of the main tissues involved in uptake of glucose under the stimulation of insulin, WAT plays very important role in metabolic and homeostasis regulation. We performed a differential proteomics study to investigate alterations in epididymis fat pad of high fat diet fed T2D KKAy mice compared to normal fed C57BL/6J mice, by 18 O-labeling relative quantitative technique. Among 329 confidently identified proteins, 121 proteins showed significant changes with CV ≤ 20% (fold changes of >2 or <0.5 as threshold). According to GO classification, we found that altered proteins contained members of biological processes of metabolic process, oxidative stress, ion homeostasis, apoptosis and cell division. In metabolic, proteins assigned to fatty acid biosynthesis (FAS etc.) were decreased, the key enzyme (ACOX3) in β-oxidation process was increased. Increased glycolysis enzymes (ENOB etc.) and decreased TCA cycle related enzymes (SCOT1 etc.) suggested that glucose metabolism in mitochondria of T2D mice might be impaired. Elevated oxidative stress was observed with alterations of a series of oxidordeuctase (QSOX1 etc.). Besides, alterations of ion homeostasis (AT2C1 etc.) proteins were also observed. The enhancement of cell proliferation associated proteins (ELYS etc.) and inhibition of apoptosis associated proteins (RASF6 etc.) in WAT might contributed to the fat pad and body weight gain. Overall, these changes in WAT may serve as a reference for understanding the functional mechanism of T2D.
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Affiliation(s)
- Ming Ke
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
| | - Hanyan Wu
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
| | - Zhaoyang Zhu
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
| | - Chi Zhang
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
| | - Yongqian Zhang
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
| | - Yunlin Deng
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
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27
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Stenemo M, Nowak C, Byberg L, Sundström J, Giedraitis V, Lind L, Ingelsson E, Fall T, Ärnlöv J. Circulating proteins as predictors of incident heart failure in the elderly. Eur J Heart Fail 2017; 20:55-62. [PMID: 28967680 DOI: 10.1002/ejhf.980] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/30/2017] [Accepted: 07/29/2017] [Indexed: 12/20/2022] Open
Abstract
AIMS To identify novel risk markers for incident heart failure using proteomic profiling of 80 proteins previously associated with cardiovascular pathology. METHODS AND RESULTS Proteomic profiling (proximity extension assay) was performed in two community-based prospective cohorts of elderly individuals without heart failure at baseline: the Prospective Investigation of the Vasculature in Uppsala Seniors [PIVUS, n = 901, median age 70.2 (interquartile range 70.0-70.3) years, 80 events]; and the Uppsala Longitudinal Study of Adult Men [ULSAM, n = 685, median age 77.8 (interquartile range 76.9-78.1) years, 90 events]. Twenty-nine proteins were associated with incident heart failure in the discovery cohort PIVUS after adjustment for age and sex, and correction for multiple testing. Eighteen associations replicated in ULSAM. In pooled analysis of both cohorts, higher levels of nine proteins were associated with incident heart failure after adjustment for established risk factors: growth differentiation factor 15 (GDF-15), T-cell immunoglobulin and mucin domain 1 (TIM-1), tumour necrosis factor-related apoptosis-inducing ligand receptor 2 (TRAIL-R2), spondin-1 (SPON1), matrix metalloproteinase-12 (MMP-12), follistatin (FS), urokinase-type plasminogen activator surface receptor (U-PAR), osteoprotegerin (OPG), and suppression of tumorigenicity 2 (ST2). Of these, GDF-15, U-PAR, MMP-12, TRAIL-R2, SPON1 and FS were associated with worsened echocardiographic left ventricular systolic function at baseline, while only TIM-1 was positively associated with worsened diastolic function (P < 0.02 for all). CONCLUSION Proteomic profiling identified several novel associations between proteins involved in apoptosis, inflammation, matrix remodelling, and fibrinolysis with incident heart failure in elderly individuals. Our results encourage additional studies investigating the underlying mechanisms and the clinical utility of our findings.
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Affiliation(s)
- Markus Stenemo
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Christoph Nowak
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Liisa Byberg
- Department of Surgical Sciences, Orthopedics, Uppsala University, Uppsala, Sweden
| | - Johan Sundström
- Uppsala Clinical Research Centre, Uppsala University, Uppsala, Sweden.,Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Ärnlöv
- School of Health and Social Studies, Dalarna University, Falun, Sweden.,Division of Family Medicine and Primary Care, Department of Neurobiology, Care Science and Society, Karolinska Institutet, Huddinge, Sweden
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28
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Liu X, Guo Z, Sun H, Li W, Sun W. Comprehensive Map and Functional Annotation of Human Pituitary and Thyroid Proteome. J Proteome Res 2017; 16:2680-2691. [PMID: 28678506 DOI: 10.1021/acs.jproteome.6b00914] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Knowledge about human tissue proteome will provide insights into health organ physiology. To construct a comprehensive data set of human pituitary and thyroid proteins, post-mortem pituitaries and thyroids from 10 normal individuals were used. The pooled samples were prepared using two methods. One part of the sample was processed using 14 high-abundance proteins immunoaffinity column. The other part was directly subjected to digestion. Finally, a total of 7596 proteins in pituitary and 5602 proteins in thyroid with high confidence were identified, with 6623 and 4368 quantified, respectively. A total of 5781 of pituitary and 3178 of thyroid proteins have not been previously reported in the normal pituitary and thyroid proteome. Comparison of pituitary and thyroid proteome indicated that thyroid prefers to be involved in nerve system regeneration and metabolic regulation, while pituitary mainly performs functions of signal transduction and cancer modulation. Our results, for the first time, comprehensively profiled and functionally annotated the largest high-confidence data set of proteome of two important endocrine glands, pituitary and thyroid, which is important for further studies on biomarker identification and molecular mechanisms of pituitary and thyroid disorders. The mapping results can be freely downloaded at http://www.urimarker.com/pituitary/ and http://www.urimarker.com/thyroid/ . The raw data are available via ProteomeXchange with identifier PXD006471.
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Affiliation(s)
- Xiaoyan Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Zhengguang Guo
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Haidan Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Wenting Li
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Wei Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
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29
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Reeve E, Trenaman SC, Rockwood K, Hilmer SN. Pharmacokinetic and pharmacodynamic alterations in older people with dementia. Expert Opin Drug Metab Toxicol 2017; 13:651-668. [DOI: 10.1080/17425255.2017.1325873] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Emily Reeve
- NHMRC Cognitive Decline Partnership Centre, Kolling Institute of Medical Research, Northern Clinical School, Faculty of Medicine, University of Sydney, Sydney, Australia
- Geriatric Medicine Research, Faculty of Medicine, Dalhousie University and Nova Scotia Health Authority, Halifax, NS, Canada
| | - Shanna C Trenaman
- Dalhousie University and Nova Scotia Health Authority, Halifax, NS, Canada
| | - Kenneth Rockwood
- Geriatric Medicine Research, Faculty of Medicine, Dalhousie University and Nova Scotia Health Authority, Halifax, NS, Canada
- Division of Geriatric Medicine, Dalhousie University, Halifax, NS, Canada
- DGI Clinical Inc., Halifax, Canada
| | - Sarah N Hilmer
- NHMRC Cognitive Decline Partnership Centre, Kolling Institute of Medical Research, Northern Clinical School, Faculty of Medicine, University of Sydney, Sydney, Australia
- Departments of Aged Care and Clinical Pharmacology, Royal North Shore Hospital, St Leonards, NSW, Australia
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30
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Keshavan A, Heslegrave A, Zetterberg H, Schott JM. Blood Biomarkers for Alzheimer's Disease: Much Promise, Cautious Progress. Mol Diagn Ther 2017; 21:13-22. [PMID: 27738910 DOI: 10.1007/s40291-016-0241-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Biomarkers in Alzheimer's disease (AD) have the potential to allow early and more accurate diagnosis, predict disease progression, stratify individuals and track response to candidate therapies in drug trials. The first fluid biomarkers reflecting aspects of AD neuropathology were identified in cerebrospinal fluid (CSF) in the 1990s. Three CSF biomarkers (amyloid-β 1-42, total tau and phospho-tau) have consistently been shown to have diagnostic utility and are incorporated into the new diagnostic criteria for AD. These markers have also been shown in longitudinal studies to predict conversion of mild cognitive impairment to AD. However, a key issue with the use of CSF biomarkers as a screening test is the invasiveness of lumbar puncture. Over the last 20 years there has been an active quest for blood biomarkers, which could be easily acquired and tested repeatedly throughout the disease course. One approach to identifying such markers is to attempt to measure candidates that have already been identified in CSF. Until recently, this approach has been limited by assay sensitivity, but newer platforms now allow single molecule-level detection. Another approach is identification of candidates in large multiplex panels that allow for multiple analytes to be quantified in parallel. While both approaches show promise, to date no blood-based biomarker or combination of biomarkers has sufficient predictive value to have utility in clinical practice. In this review, an overview of promising blood protein candidates is provided, and the challenges of validating and converting these into practicable tests are discussed.
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Affiliation(s)
- Ashvini Keshavan
- Dementia Research Centre, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Box 16, Queen Square, London, WC1N 3BG, UK
| | - Amanda Heslegrave
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Henrik Zetterberg
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Sahlgrenska University Hospital, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Jonathan M Schott
- Dementia Research Centre, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Box 16, Queen Square, London, WC1N 3BG, UK.
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31
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The Role of Chromatography in Alzheimer’s Disease Drug Discovery. ADVANCES IN CHROMATOGRAPHY 2016. [DOI: 10.1201/9781315370385-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Khan AT, Dobson RJB, Sattlecker M, Kiddle SJ. Alzheimer's disease: are blood and brain markers related? A systematic review. Ann Clin Transl Neurol 2016; 3:455-62. [PMID: 27547773 PMCID: PMC4891999 DOI: 10.1002/acn3.313] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/29/2016] [Accepted: 04/07/2016] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE Peripheral protein biomarkers of Alzheimer's disease (AD) may help identify novel treatment avenues by allowing early diagnosis, recruitment to clinical trials, and treatment initiation. The purpose of this review was to determine which proteins have been found to be differentially expressed in the AD brain and whether these proteins are also found within the blood of AD patients. METHODS A two-stage approach was conducted. The first stage involved conducting a systematic search to identify discovery-based brain proteomic studies of AD. The second stage involved comparing whether proteins found to be differentially expressed in AD brain were also differentially expressed in the blood. RESULTS Across 11 discovery based brain proteomic studies 371 proteins were at different levels in the AD brain. Nine proteins were frequently found, defined as appearing in at least three separate studies. Of these proteins heat-shock cognate 71 kDa, ubiquitin carboxyl-terminal hydrolase isozyme L1, and 2',3'-cyclic nucleotide 3' phosphodiesterase alone were found to share a consistent direction of change, being consistently upregulated in studies they appeared in. Eighteen proteins seen as being differentially expressed within the AD brain were present in blood proteomic studies of AD. Only complement C4a was seen multiple times within both the blood and brain proteomic studies. INTERPRETATION We report a number of proteins appearing in both the blood and brain of AD patients. Of these proteins, C4a may be a good candidate for further follow-up in large-scale replication efforts.
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Affiliation(s)
- Ali T. Khan
- GKT School of Medical EducationKing's College LondonLondonUnited Kingdom
| | - Richard J. B. Dobson
- MRC Social, Genetic and Developmental Psychiatry CentreInstitute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUnited Kingdom
- NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for DementiaLondonUnited Kingdom
| | - Martina Sattlecker
- MRC Social, Genetic and Developmental Psychiatry CentreInstitute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUnited Kingdom
- NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for DementiaLondonUnited Kingdom
| | - Steven J. Kiddle
- MRC Social, Genetic and Developmental Psychiatry CentreInstitute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUnited Kingdom
- NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for DementiaLondonUnited Kingdom
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Serum Levels of ApoA1 and ApoA2 Are Associated with Cognitive Status in Older Men. BIOMED RESEARCH INTERNATIONAL 2015; 2015:481621. [PMID: 26682220 PMCID: PMC4670907 DOI: 10.1155/2015/481621] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 11/04/2015] [Accepted: 11/08/2015] [Indexed: 01/02/2023]
Abstract
Background. Advancing age, chronic inflammation, oxidative damage, and disorders of lipid metabolism are positively linked to the late-life cognitive impairment. Serum biomarkers may be associated with the cognitive status in older men. Methods. 440 old male subjects with different cognitive functions were recruited to investigate probable serum markers. Pearson Chi-Squared test, univariate analysis, and multivariate logistic regression analysis were performed to evaluate biomarkers which may be associated with cognitive status. Results. Levels of fundus atherosclerosis (AS) (P < 0.001), age (P < 0.001), serum biomarkers peroxidase (POD) (P = 0.026) and interleukin-6 (IL-6) (P = 0.001), serum levels of high-density lipoprotein cholesterol (HDL-C) (P < 0.001), apolipoprotein A2 (ApoA2) (P = 0.001), and ApoC2 (P = 0.005) showed significant differences. Compared to group 3, ApoA1 in group 1 (OR = 1.30, 95% CI 1.01–1.67) and group 2 (OR = 1.47, 95% CI 1.11–1.94) were higher, while ApoA2 were lower (group 1: OR = 0.43, 95% CI 0.18–1.02; group 2: OR = 0.21, 95% CI 0.08–0.54) after adjusting for control variables. Conclusion. The results demonstrated that age, AS levels, POD, IL-6, HDL-C, ApoA2, and ApoC2 were significantly related to cognitive status. Moreover, ApoA1 and ApoA2 were independently associated with cognitive impairment and late-life dementia.
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Baird AL, Westwood S, Lovestone S. Blood-Based Proteomic Biomarkers of Alzheimer's Disease Pathology. Front Neurol 2015; 6:236. [PMID: 26635716 PMCID: PMC4644785 DOI: 10.3389/fneur.2015.00236] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/26/2015] [Indexed: 12/31/2022] Open
Abstract
The complexity of Alzheimer’s disease (AD) and its long prodromal phase poses challenges for early diagnosis and yet allows for the possibility of the development of disease modifying treatments for secondary prevention. It is, therefore, of importance to develop biomarkers, in particular, in the preclinical or early phases that reflect the pathological characteristics of the disease and, moreover, could be of utility in triaging subjects for preventative therapeutic clinical trials. Much research has sought biomarkers for diagnostic purposes by comparing affected people to unaffected controls. However, given that AD pathology precedes disease onset, a pathology endophenotype design for biomarker discovery creates the opportunity for detection of much earlier markers of disease. Blood-based biomarkers potentially provide a minimally invasive option for this purpose and research in the field has adopted various “omics” approaches in order to achieve this. This review will, therefore, examine the current literature regarding blood-based proteomic biomarkers of AD and its associated pathology.
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Affiliation(s)
- Alison L Baird
- Department of Psychiatry, University of Oxford , Oxford , UK
| | - Sarah Westwood
- Department of Psychiatry, University of Oxford , Oxford , UK
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford , Oxford , UK
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Liang HC, Russell C, Mitra V, Chung R, Hye A, Bazenet C, Lovestone S, Pike I, Ward M. Glycosylation of Human Plasma Clusterin Yields a Novel Candidate Biomarker of Alzheimer’s Disease. J Proteome Res 2015; 14:5063-76. [DOI: 10.1021/acs.jproteome.5b00892] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hui-Chung Liang
- Proteome Sciences plc, Coveham
House, Downside Bridge Road, Cobham KT11 3EP, United Kingdom
| | - Claire Russell
- Proteome Sciences plc, Coveham
House, Downside Bridge Road, Cobham KT11 3EP, United Kingdom
| | - Vikram Mitra
- Proteome Sciences plc, Coveham
House, Downside Bridge Road, Cobham KT11 3EP, United Kingdom
| | - Raymond Chung
- Department
of Old Age Psychiatry, Institute of Psychiatry, King’s College London, De Crespigny Park, London SE5 8AF, United Kingdom
| | - Abdul Hye
- Department
of Old Age Psychiatry, Institute of Psychiatry, King’s College London, De Crespigny Park, London SE5 8AF, United Kingdom
| | - Chantal Bazenet
- Department
of Old Age Psychiatry, Institute of Psychiatry, King’s College London, De Crespigny Park, London SE5 8AF, United Kingdom
| | - Simon Lovestone
- Department
of Psychiatry, Medical Sciences Division, University of Oxford, Warneford Hospital, Oxford OX3 7JX, United Kingdom
| | - Ian Pike
- Proteome Sciences plc, Coveham
House, Downside Bridge Road, Cobham KT11 3EP, United Kingdom
| | - Malcolm Ward
- Proteome Sciences plc, Coveham
House, Downside Bridge Road, Cobham KT11 3EP, United Kingdom
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Shah DJ, Rohlfing F, Anand S, Johnson WE, Alvarez MTB, Cobell J, King J, Young SA, Kauwe JS, Graves SW. Discovery and Subsequent Confirmation of Novel Serum Biomarkers Diagnosing Alzheimer’s Disease. J Alzheimers Dis 2015; 49:317-27. [DOI: 10.3233/jad-150498] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Dipti Jigar Shah
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | | | - Swati Anand
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - W. Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston University, Boston, MA, USA
| | | | - Jesse Cobell
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Jackson King
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Sydney A. Young
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - John S.K. Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Steven W. Graves
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
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García-Fontana B, Morales-Santana S, Longobardo V, Reyes-García R, Rozas-Moreno P, García-Salcedo JA, Muñoz-Torres M. Relationship between Proinflammatory and Antioxidant Proteins with the Severity of Cardiovascular Disease in Type 2 Diabetes Mellitus. Int J Mol Sci 2015; 16:9469-83. [PMID: 25923078 PMCID: PMC4463599 DOI: 10.3390/ijms16059469] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/01/2015] [Accepted: 04/08/2015] [Indexed: 02/05/2023] Open
Abstract
Type 2 diabetes mellitus patients are at significant risk of cardiovascular disease, however, the pathophysiology of these complications is complex and incompletely known in this population. The aim of this study was to compare the serum proteome of patients with type 2 diabetes mellitus presenting or not presenting cardiovascular disease with non-diabetic subjects to find essential proteins related to these cardiovascular complications. This cross-sectional study compares the serum proteome by a combination of protein depletion with 2D-DIGE (2-dimension Difference Gel Electrophoresis) methodology. The proteins differentially expressed were identified by MALDI TOF/TOF (Matrix-assisted laser desorption/ionization and Time-Of-Flight ion detector) or LC-MS/MS (Liquid Chromatography coupled to Mass-Mass Spectrometry). Type 2 diabetes mellitus patients with cardiovascular disease showed higher expression of plasma retinol binding protein and glutathione peroxidase-3 compared to those without cardiovascular disease and non-diabetic controls. These results show that proteins related to the inflammatory and redox state appear to play an important role in the pathogenesis of the cardiovascular disease in the type 2 diabetes mellitus patients.
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Affiliation(s)
- Beatriz García-Fontana
- Bone Metabolic Unit, Endocrinology Division (RETICEF), Instituto de Investigación Biosanitaria (Ibs) Granada, University Hospital San Cecilio, Granada 18012, Spain.
| | - Sonia Morales-Santana
- Bone Metabolic Unit, Endocrinology Division (RETICEF), Instituto de Investigación Biosanitaria (Ibs) Granada, University Hospital San Cecilio, Granada 18012, Spain.
- Proteomic Research Service, Instituto de Investigación Biosanitaria (Ibs) Granada, University Hospital San Cecilio, Granada 18012, Spain.
| | - Victoria Longobardo
- Proteomic Research Service, Institute of Parasitology and Biomedicine "López Neyra" (C.S.I.C.), Granada 18016, Spain.
| | - Rebeca Reyes-García
- Bone Metabolic Unit, Endocrinology Division (RETICEF), Instituto de Investigación Biosanitaria (Ibs) Granada, University Hospital San Cecilio, Granada 18012, Spain.
| | - Pedro Rozas-Moreno
- Endocrinology Division, Ciudad Real General Hospital, Ciudad Real 13005, Spain.
| | - José Antonio García-Salcedo
- Infectious Diseases Unit, Instituto de Investigación Biosanitaria (Ibs) Granada, University Hospital San Cecilio, Av. Dr. Olóriz 16, Granada 18012, Spain.
| | - Manuel Muñoz-Torres
- Bone Metabolic Unit, Endocrinology Division (RETICEF), Instituto de Investigación Biosanitaria (Ibs) Granada, University Hospital San Cecilio, Granada 18012, Spain.
- Endocrinology Unit, University Hospital San Cecilio, Av. Dr. Olóriz 16, Granada 18012, Spain.
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Jayasena T, Poljak A, Braidy N, Smythe G, Raftery M, Hill M, Brodaty H, Trollor J, Kochan N, Sachdev P. Upregulation of glycolytic enzymes, mitochondrial dysfunction and increased cytotoxicity in glial cells treated with Alzheimer's disease plasma. PLoS One 2015; 10:e0116092. [PMID: 25785936 PMCID: PMC4364672 DOI: 10.1371/journal.pone.0116092] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 12/04/2014] [Indexed: 11/19/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder associated with increased oxidative stress and neuroinflammation. Markers of increased protein, lipid and nucleic acid oxidation and reduced activities of antioxidant enzymes have been reported in AD plasma. Amyloid plaques in the AD brain elicit a range of reactive inflammatory responses including complement activation and acute phase reactions, which may also be reflected in plasma. Previous studies have shown that human AD plasma may be cytotoxic to cultured cells. We investigated the effect of pooled plasma (n = 20 each) from healthy controls, individuals with amnestic mild cognitive impairment (aMCI) and Alzheimer's disease (AD) on cultured microglial cells. AD plasma and was found to significantly decrease cell viability and increase glycolytic flux in microglia compared to plasma from healthy controls. This effect was prevented by the heat inactivation of complement. Proteomic methods and isobaric tags (iTRAQ) found the expression level of complement and other acute phase proteins to be altered in MCI and AD plasma and an upregulation of key enzymes involved in the glycolysis pathway in cells exposed to AD plasma. Altered expression levels of acute phase reactants in AD plasma may alter the energy metabolism of glia.
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Affiliation(s)
- Tharusha Jayasena
- Bioanalytical Mass Spectrometry Facility, MW Analytical Centre, University of New South Wales, Sydney, Australia
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
| | - Anne Poljak
- Bioanalytical Mass Spectrometry Facility, MW Analytical Centre, University of New South Wales, Sydney, Australia
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
- * E-mail:
| | - Nady Braidy
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
| | - George Smythe
- Bioanalytical Mass Spectrometry Facility, MW Analytical Centre, University of New South Wales, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Mark Raftery
- Bioanalytical Mass Spectrometry Facility, MW Analytical Centre, University of New South Wales, Sydney, Australia
| | - Mark Hill
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Henry Brodaty
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
- Dementia Collaborative Research Centre, University of New South Wales, Sydney, Australia
| | - Julian Trollor
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
- Neuropsychiatric Institute, the Prince of Wales Hospital, Sydney, Australia
| | - Nicole Kochan
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
- Neuropsychiatric Institute, the Prince of Wales Hospital, Sydney, Australia
| | - Perminder Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
- Neuropsychiatric Institute, the Prince of Wales Hospital, Sydney, Australia
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An anemia of Alzheimer's disease. Mol Psychiatry 2014; 19:1227-34. [PMID: 24419041 DOI: 10.1038/mp.2013.178] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 10/03/2013] [Accepted: 10/29/2013] [Indexed: 01/22/2023]
Abstract
Lower hemoglobin is associated with cognitive impairment and Alzheimer's disease (AD). Since brain iron homeostasis is perturbed in AD, we investigated whether this is peripherally reflected in the hematological and related blood chemistry values from the Australian Imaging Biomarker and Lifestyle (AIBL) study (a community-based, cross-sectional cohort comprising 768 healthy controls (HC), 133 participants with mild cognitive impairment (MCI) and 211 participants with AD). We found that individuals with AD had significantly lower hemoglobin, mean cell hemoglobin concentrations, packed cell volume and higher erythrocyte sedimentation rates (adjusted for age, gender, APOE-ɛ4 and site). In AD, plasma iron, transferrin, transferrin saturation and red cell folate levels exhibited a significant distortion of their customary relationship to hemoglobin levels. There was a strong association between anemia and AD (adjusted odds ratio (OR)=2.43, confidence interval (CI) (1.31, 4.54)). Moreover, AD emerged as a strong risk factor for anemia on step-down regression, even when controlling for all other available explanations for anemia (adjusted OR=3.41, 95% CI (1.68, 6.92)). These data indicated that AD is complicated by anemia, which may itself contribute to cognitive decline.
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Sattlecker M, Kiddle SJ, Newhouse S, Proitsi P, Nelson S, Williams S, Johnston C, Killick R, Simmons A, Westman E, Hodges A, Soininen H, Kłoszewska I, Mecocci P, Tsolaki M, Vellas B, Lovestone S, Dobson RJB. Alzheimer's disease biomarker discovery using SOMAscan multiplexed protein technology. Alzheimers Dement 2014; 10:724-34. [PMID: 24768341 DOI: 10.1016/j.jalz.2013.09.016] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 09/06/2013] [Accepted: 09/24/2013] [Indexed: 12/26/2022]
Abstract
Blood proteins and their complexes have become the focus of a great deal of interest in the context of their potential as biomarkers of Alzheimer's disease (AD). We used a SOMAscan assay for quantifying 1001 proteins in blood samples from 331 AD, 211 controls, and 149 mild cognitive impaired (MCI) subjects. The strongest associations of protein levels with AD outcomes were prostate-specific antigen complexed to α1-antichymotrypsin (AD diagnosis), pancreatic prohormone (AD diagnosis, left entorhinal cortex atrophy, and left hippocampus atrophy), clusterin (rate of cognitive decline), and fetuin B (left entorhinal atrophy). Multivariate analysis found that a subset of 13 proteins predicted AD with an accuracy of area under the curve of 0.70. Our replication of previous findings provides further evidence that levels of these proteins in plasma are truly associated with AD. The newly identified proteins could be potential biomarkers and are worthy of further investigation.
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Affiliation(s)
- Martina Sattlecker
- King's College London, Institute of Psychiatry, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation Trust, London, UK
| | - Steven J Kiddle
- King's College London, Institute of Psychiatry, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation Trust, London, UK
| | - Stephen Newhouse
- King's College London, Institute of Psychiatry, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation Trust, London, UK
| | - Petroula Proitsi
- King's College London, Institute of Psychiatry, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation Trust, London, UK
| | | | | | - Caroline Johnston
- King's College London, Institute of Psychiatry, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation Trust, London, UK
| | - Richard Killick
- King's College London, Institute of Psychiatry, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation Trust, London, UK
| | - Andrew Simmons
- King's College London, Institute of Psychiatry, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation Trust, London, UK
| | - Eric Westman
- King's College London, Institute of Psychiatry, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation Trust, London, UK
| | - Angela Hodges
- King's College London, Institute of Psychiatry, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation Trust, London, UK
| | - Hilkka Soininen
- Department of Neurology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Patrizia Mecocci
- Institute of Gerontology and Geriatrics, University of Perugia, Perugia, Italy
| | - Magda Tsolaki
- 3rd Department of Neurology, Aristotle University, Thessaloniki, Greece
| | - Bruno Vellas
- INSERM U 558, University of Toulouse, Toulouse, France
| | - Simon Lovestone
- King's College London, Institute of Psychiatry, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation Trust, London, UK
| | - Richard J B Dobson
- King's College London, Institute of Psychiatry, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation Trust, London, UK.
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Fu Y, Zhao D, Yang L. Protein-Based Biomarkers in Cerebrospinal Fluid and Blood for Alzheimer’s Disease. J Mol Neurosci 2014; 54:739-47. [DOI: 10.1007/s12031-014-0356-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 06/11/2014] [Indexed: 12/21/2022]
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Biomarkers in Alzheimer's disease analysis by mass spectrometry-based proteomics. Int J Mol Sci 2014; 15:7865-82. [PMID: 24806343 PMCID: PMC4057708 DOI: 10.3390/ijms15057865] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 04/03/2014] [Accepted: 04/09/2014] [Indexed: 01/07/2023] Open
Abstract
Alzheimer’s disease (AD) is a common chronic and destructive disease. The early diagnosis of AD is difficult, thus the need for clinically applicable biomarkers development is growing rapidly. There are many methods to biomarker discovery and identification. In this review, we aim to summarize Mass spectrometry (MS)-based proteomics studies on AD and discuss thoroughly the methods to identify candidate biomarkers in cerebrospinal fluid (CSF) and blood. This review will also discuss the potential research areas on biomarkers.
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Pavlovic Z, Zhu L, Pereira L, Singh RK, Cornell RB, Bakovic M. Isoform-specific and protein kinase C-mediated regulation of CTP:phosphoethanolamine cytidylyltransferase phosphorylation. J Biol Chem 2014; 289:9053-64. [PMID: 24519946 DOI: 10.1074/jbc.m113.544932] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CTP:phosphoethanolamine cytidylyltransferase (Pcyt2) is the main regulatory enzyme for de novo biosynthesis of phosphatidylethanolamine by the CDP-ethanolamine pathway. There are two isoforms of Pcyt2, -α and -β; however, very little is known about their specific roles in this important metabolic pathway. We previously demonstrated increased phosphatidylethanolamine biosynthesis subsequent to elevated activity and phosphorylation of Pcyt2α and -β in MCF-7 breast cancer cells grown under conditions of serum deficiency. Mass spectroscopy analyses of Pcyt2 provided evidence for isoform-specific as well as shared phosphorylations. Pcyt2β was specifically phosphorylated at the end of the first cytidylyltransferase domain. Pcyt2α was phosphorylated within the α-specific motif that is spliced out in Pcyt2β and on two PKC consensus serine residues, Ser-215 and Ser-223. Single and double mutations of PKC consensus sites reduced Pcyt2α phosphorylation, activity, and phosphatidylethanolamine synthesis by 50-90%. The phosphorylation and activity of endogenous Pcyt2 were dramatically increased with phorbol esters and reduced by specific PKC inhibitors. In vitro translated Pcyt2α was phosphorylated by PKCα, PKCβI, and PKCβII. Pcyt2α Ser-215 was also directly phosphorylated with PKCα. Mapping of the Pcyt2α- and -β-phosphorylated sites to the solved structure of a human Pcyt2β showed that they clustered within and flanking the central linker region that connects the two catalytic domains and is a novel regulatory segment not present in other cytidylyltransferases. This study is the first to demonstrate differences in phosphorylation between Pcyt2 isoforms and to uncover the role of the PKC-regulated phosphorylation.
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Affiliation(s)
- Zvezdan Pavlovic
- From the Department of Human Health and Nutritional Sciences, University of Guelph, Ontario N1G 2W1 and
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Song F, Poljak A, Kochan NA, Raftery M, Brodaty H, Smythe GA, Sachdev PS. Plasma protein profiling of Mild Cognitive Impairment and Alzheimer's disease using iTRAQ quantitative proteomics. Proteome Sci 2014; 12:5. [PMID: 24433274 PMCID: PMC3898732 DOI: 10.1186/1477-5956-12-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/10/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND With the promise of disease modifying treatments, there is a need for more specific diagnosis and prognosis of Alzheimer's disease (AD) and mild cognitive impairment (MCI). Plasma biomarkers are likely to be utilised to increase diagnostic accuracy and specificity of AD and cognitive decline. METHODS Isobaric tags (iTRAQ) and proteomic methods were used to identify potential plasma biomarkers of MCI and AD. Relative protein expression level changes were quantified in plasma of 411 cognitively normal subjects, 19 AD patients and 261 MCI patients. Plasma was pooled into 4 groups including normal control, AD, amnestic single and multiple domain MCI (aMCI), and nonamnestic single and multiple domain MCI (nMCI). Western-blotting was used to validate iTRAQ data. Integrated function and protein interactions were explored using WEB based bioinformatics tools (DAVID v6.7 and STRING v9.0). RESULTS In at least two iTRAQ replicate experiments, 30 proteins were significantly dysregulated in MCI and AD plasma, relative to controls. These proteins included ApoA1, ApoB100, complement C3, C4b-binding protein, afamin, vitamin D-binding protein precursor, isoform 1 of Gelsolin actin regulator, Ig mμ chain C region (IGHM), histidine-rich glycoprotein and fibrinogen β and γ chains. Western-blotting confirmed that afamin was decreased and IGHM was increased in MCI and AD groups. Bioinformatics results indicated that these dysregulated proteins represented a diversity of biological processes, including acute inflammatory response, cholesterol transport and blood coagulation. CONCLUSION These findings demonstrate that expression level changes in multiple proteins are observed in MCI and AD plasma. Some of these, such as afamin and IGHM, may be candidate biomarkers for AD and the predementia condition of MCI.
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Affiliation(s)
| | - Anne Poljak
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, Australia.
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45
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Sheta EA, Appel SH, Goldknopf IL. 2D gel blood serum biomarkers reveal differential clinical proteomics of the neurodegenerative diseases. Expert Rev Proteomics 2014; 3:45-62. [PMID: 16445350 DOI: 10.1586/14789450.3.1.45] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This review addresses the challenges of neuroproteomics and recent progress in biomarkers and tests for neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. The review will discuss how the application of quantitative 2D gel electrophoresis, combined with appropriate single-variable and multivariate biostatistics, allows for selection of disease-specific serum biomarkers. It will also address how the use of large cohorts of specifically targeted patient blood serum samples and complimentary age-matched controls, in parallel with the use of selected panels of these biomarkers, are being applied to the development of blood tests to specifically address unmet pressing needs in the differential diagnosis of these diseases, and to provide potential avenues for mechanism-based drug targeting and treatment monitoring. While exploring recent findings in this area, the review discusses differences in critical pathways of immune/inflammation and amyloid formation between Parkinson's disease and amyotrophic lateral sclerosis, as well as discernable synergistic relationships between these pathways that are revealed by this approach. The potential for pathway measurement in blood tests for differential diagnosis, disease burden and therapeutic monitoring is also outlined.
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Affiliation(s)
- Essam A Sheta
- Power3 Medical Products, Inc., The Woodlands, TX 77381, USA.
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Millard SP, Lutz F, Li G, Galasko DR, Farlow MR, Quinn JF, Kaye JA, Leverenz JB, Tsuang D, Yu CE, Peskind ER, Bekris LM. Association of cerebrospinal fluid Aβ42 with A2M gene in cognitively normal subjects. Neurobiol Aging 2013; 35:357-64. [PMID: 24011543 DOI: 10.1016/j.neurobiolaging.2013.07.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 12/17/2022]
Abstract
Low cerebrospinal fluid (CSF) Aβ(42) levels correlate with increased brain Aβ deposition in Alzheimer's disease (AD), which suggests a disruption in the degradation and clearance of Aβ from the brain. In addition, APOE ε4 carriers have lower CSF Aβ(42) levels than non-carriers. The hypothesis of this investigation was that CSF Aβ(42) levels would correlate with regulatory region variation in genes that are biologically associated with degradation or clearance of Aβ from the brain. CSF Aβ(42) levels were tested for associations with Aβ degradation and clearance genes and APOE ε4. Twenty-four SNPs located within the 5' and 3' regions of 12 genes were analyzed. The study sample consisted of 99 AD patients and 168 cognitively normal control subjects. CSF Aβ(42) levels were associated with APOE ε4 status in controls but not in AD patients; A2M regulatory region SNPs were also associated with CSF Aβ(42) levels in controls but not in AD patients, even after adjusting for APOE ε4. These results suggest that genetic variation within the A2M gene influences CSF Aβ(42) levels.
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Affiliation(s)
- Steven P Millard
- Northwest Network VISN-20 Mental Illness Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA.
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Cornelis MC, Hu FB. Systems Epidemiology: A New Direction in Nutrition and Metabolic Disease Research. Curr Nutr Rep 2013; 2. [PMID: 24278790 DOI: 10.1007/s13668-013-0052-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Systems epidemiology applied to the field of nutrition has potential to provide new insight into underlying mechanisms and ways to study the health effects of specific foods more comprehensively. Human intervention and population-based studies have identified i) common genetic factors associated with several nutrition-related traits and ii) dietary factors altering the expression of genes and levels of proteins and metabolites related to inflammation, lipid metabolism and/or gut microbial metabolism, results of high relevance to metabolic disease. System-level tools applied type 2 diabetes and related conditions have revealed new pathways that are potentially modified by diet and thus offer additional opportunities for nutritional investigations. Moving forward, harnessing the resources of existing large prospective studies within which biological samples have been archived and diet and lifestyle have been measured repeatedly within individual will enable systems-level data to be integrated, the outcome of which will be improved personalized optimal nutrition for prevention and treatment of disease.
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Affiliation(s)
- Marilyn C Cornelis
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
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Rembach A, Ryan TM, Roberts BR, Doecke JD, Wilson WJ, Watt AD, Barnham KJ, Masters CL. Progress towards a consensus on biomarkers for Alzheimer’s disease: a review of peripheral analytes. Biomark Med 2013; 7:641-62. [DOI: 10.2217/bmm.13.59] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common cause of dementia in the elderly population and attempts to develop therapies have been unsuccessful because there is no means to target an effective therapeutic window. CNS biomarkers are insightful but impractical for high-throughput population-based screening. Therefore, a peripheral, blood-based biomarker for AD would significantly improve early diagnosis, potentially enable presymptomatic detection and facilitate effective targeting of disease-modifying treatments. The various constituents of blood, including plasma, platelets and cellular fractions, are now being systematically explored as a pool of putative peripheral biomarkers for AD. In this review we cover some less known peripheral biomarkers and highlight the latest developments for their clinical application.
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Affiliation(s)
- Alan Rembach
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia.
| | - Tim M Ryan
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia
| | - Blaine R Roberts
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia
| | - James D Doecke
- The Australian e-Health Research Centre, Herston, Queensland, 4029, Australia
- CSIRO Preventative Health National Research Flagship, North Ryde, New South Wales, 2113, Australia
| | - William J Wilson
- CSIRO Preventative Health National Research Flagship, North Ryde, New South Wales, 2113, Australia
| | - Andrew D Watt
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia
| | - Kevin J Barnham
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia
| | - Colin L Masters
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia
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Gupta VB, Sundaram R, Martins RN. Multiplex biomarkers in blood. ALZHEIMERS RESEARCH & THERAPY 2013; 5:31. [PMID: 23795953 PMCID: PMC3707019 DOI: 10.1186/alzrt185] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Advances in the field of blood biomarker discovery will help in identifying Alzheimer's disease in its preclinical stage, allowing treatment to be initiated before irreversible damage occurs. This review discusses some recent past and current approaches being taken by researchers in the field. Individual blood biomarkers have been unsuccessful in defining the disease pathology, progression and thus diagnosis. This directs to the need for discovering a multiplex panel of blood biomarkers as a promising approach with high sensitivity and specificity for early diagnosis. However, it is a great challenge to standardize a worldwide blood biomarker panel due to the innate differences in the population tested, nature of the samples and methods utilised in different studies across the globe. We highlight several issues that result in the lack of reproducibility in this field of research currently faced by researchers. Several important measures are summarized towards the end of the review that can be taken to minimize the variability among various centres.
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Affiliation(s)
- Veer Bala Gupta
- Centre of Excellence for Alzheimer's disease Research & Care, School of Medical Sciences, Edith Cowan University, Joondalup, WA, 6027 Australia
| | - Ramani Sundaram
- Centre for Ageing and Alzheimer's, Nightingales, Bangalore, 560043 India
| | - Ralph N Martins
- Centre of Excellence for Alzheimer's disease Research & Care, School of Medical Sciences, Edith Cowan University, Joondalup, WA, 6027 Australia ; Sir James McCusker Alzheimer's Disease Research Unit (Hollywood Private Hospital), Perth, WA, 6009 Australia ; Suite 22, Hollywood Medical Centre, 85 Monash Ave, Nedlands, WA, 6009 Australia
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Takahashi E, Okumura A, Unoki-Kubota H, Hirano H, Kasuga M, Kaburagi Y. Differential proteome analysis of serum proteins associated with the development of type 2 diabetes mellitus in the KK-Ay mouse model using the iTRAQ technique. J Proteomics 2013; 84:40-51. [DOI: 10.1016/j.jprot.2013.03.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 03/15/2013] [Accepted: 03/19/2013] [Indexed: 01/01/2023]
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