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Ferreira CR, Lima Gomes PCFD, Robison KM, Cooper BR, Shannahan JH. Implementation of multiomic mass spectrometry approaches for the evaluation of human health following environmental exposure. Mol Omics 2024; 20:296-321. [PMID: 38623720 PMCID: PMC11163948 DOI: 10.1039/d3mo00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings. Most of the omics instruments are operated by specialists in dedicated laboratories; however, the development of miniature portable omics has made the technology more available to users for field applications. Variations in molecular information gained from omics approaches are useful for evaluating human health following environmental exposure and the development and progression of numerous diseases. As MS technology develops so do statistical and machine learning methods for the detection of molecular deviations from personalized metabolism, which are correlated to altered health conditions, and they are intended to provide a multi-disciplinary overview for researchers interested in adding multiomic analysis to their current efforts. This includes an introduction to mass spectrometry-based omics technologies, current state-of-the-art capabilities and their respective strengths and limitations for surveying molecular information. Furthermore, we describe how knowledge gained from these assessments can be applied to personalized medicine and diagnostic strategies.
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Affiliation(s)
- Christina R Ferreira
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | | | - Kiley Marie Robison
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce R Cooper
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | - Jonathan H Shannahan
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
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2
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Nijakowski K, Owecki W, Jankowski J, Surdacka A. Salivary Biomarkers for Alzheimer's Disease: A Systematic Review with Meta-Analysis. Int J Mol Sci 2024; 25:1168. [PMID: 38256241 PMCID: PMC10817083 DOI: 10.3390/ijms25021168] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/03/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Alzheimer's Disease (AD) is the most common neurodegenerative disease which manifests with progressive cognitive impairment, leading to dementia. Considering the noninvasive collection of saliva, we designed the systematic review to answer the question "Are salivary biomarkers reliable for the diagnosis of Alzheimer's Disease?" Following the inclusion and exclusion criteria, 30 studies were included in this systematic review (according to the PRISMA statement guidelines). Potential biomarkers include mainly proteins, metabolites and even miRNAs. Based on meta-analysis, in AD patients, salivary levels of beta-amyloid42 and p-tau levels were significantly increased, and t-tau and lactoferrin were decreased at borderline statistical significance. However, according to pooled AUC, lactoferrin and beta-amyloid42 showed a significant predictive value for salivary-based AD diagnosis. In conclusion, potential markers such as beta-amyloid42, tau and lactoferrin can be detected in the saliva of AD patients, which could reliably support the early diagnosis of this neurodegenerative disease.
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Affiliation(s)
- Kacper Nijakowski
- Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland;
| | - Wojciech Owecki
- Student’s Scientific Group in Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland (J.J.)
| | - Jakub Jankowski
- Student’s Scientific Group in Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland (J.J.)
| | - Anna Surdacka
- Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland;
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3
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de Souza HMR, Pereira TTP, de Sá HC, Alves MA, Garrett R, Canuto GAB. Critical Factors in Sample Collection and Preparation for Clinical Metabolomics of Underexplored Biological Specimens. Metabolites 2024; 14:36. [PMID: 38248839 PMCID: PMC10819689 DOI: 10.3390/metabo14010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
This review article compiles critical pre-analytical factors for sample collection and extraction of eight uncommon or underexplored biological specimens (human breast milk, ocular fluids, sebum, seminal plasma, sweat, hair, saliva, and cerebrospinal fluid) under the perspective of clinical metabolomics. These samples are interesting for metabolomics studies as they reflect the status of living organisms and can be applied for diagnostic purposes and biomarker discovery. Pre-collection and collection procedures are critical, requiring protocols to be standardized to avoid contamination and bias. Such procedures must consider cleaning the collection area, sample stimulation, diet, and food and drug intake, among other factors that impact the lack of homogeneity of the sample group. Precipitation of proteins and removal of salts and cell debris are the most used sample preparation procedures. This review intends to provide a global view of the practical aspects that most impact results, serving as a starting point for the designing of metabolomic experiments.
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Affiliation(s)
- Hygor M. R. de Souza
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
| | - Tássia T. P. Pereira
- Departamento de Genética, Ecologia e Evolucao, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil
| | - Hanna C. de Sá
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
| | - Marina A. Alves
- Instituto de Pesquisa de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil;
| | - Rafael Garrett
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
- Department of Laboratory Medicine, Boston Children’s Hospital—Harvard Medical School, Boston, MA 02115, USA
| | - Gisele A. B. Canuto
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
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Zürcher C, Humpel C. Saliva: a challenging human fluid to diagnose brain disorders with a focus on Alzheimer's disease. Neural Regen Res 2023; 18:2606-2610. [PMID: 37449596 DOI: 10.4103/1673-5374.373675] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
Biomarkers are molecules of biological processes that help in both the diagnosis of human diseases and in follow-up assessments of therapeutic responses. Biomarkers can be measured in many human fluids, such as blood, cerebrospinal fluid, urine, and saliva. The -omics methods (genomics, RNomics, proteomics, and metabolomics) are useful at measuring thousands of markers in a small volume. Saliva is a human fluid that is easily accessible, without any ethical concerns. Yet, saliva remains unexplored in regard to many human disease biomarkers. In this review, we will give an overview on saliva and how it can be influenced by exogenous factors. As we focus on the potential use of saliva as a diagnostic tool in brain disorders (especially Alzheimer's disease), we will cover how saliva is linked to the brain. We will discuss that saliva is a heterogeneous human fluid, yet useful for the discovery of biomarkers in human disorders. However, a procedure and consensus that is controlled, validated, and standardized for the collection and processing of saliva is required, followed by a highly sensitive diagnostic approach.
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Affiliation(s)
- Christine Zürcher
- University Hospital for Restorative Dentistry and Periodontology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian Humpel
- Laboratory of Psychiatry & Experimental Alzheimer's Research, Department of Psychiatry I, Medical University of Innsbruck, Innsbruck, Austria
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Chang CW, Hsu JY, Hsiao PZ, Chen YC, Liao PC. Identifying Hair Biomarker Candidates for Alzheimer's Disease Using Three High Resolution Mass Spectrometry-Based Untargeted Metabolomics Strategies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:550-561. [PMID: 36973238 DOI: 10.1021/jasms.2c00294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
High-resolution mass spectrometry (HRMS)-based untargeted metabolomics strategies have emerged as an effective tool for discovering biomarkers of Alzheimer's disease (AD). There are various HRMS-based untargeted metabolomics strategies for biomarker discovery, including the data-dependent acquisition (DDA) method, the combination of full scan and target MS/MS, and the all ion fragmentation (AIF) method. Hair has emerged as a potential biospecimen for biomarker discovery in clinical research since it might reflect the circulating metabolic profiles over several months, while the analytical performances of the different data acquisition methods for hair biomarker discovery have been rarely investigated. Here, the analytical performances of three data acquisition methods in HRMS-based untargeted metabolomics for hair biomarker discovery were evaluated. The human hair samples from AD patients (N = 23) and cognitively normal individuals (N = 23) were used as an example. The most significant number of discriminatory features was acquired using the full scan (407), which is approximately 10-fold higher than that using the DDA strategy (41) and 11% higher than that using the AIF strategy (366). Only 66% of discriminatory chemicals discovered in the DDA strategy were discriminatory features in the full scan dataset. Moreover, compared to the deconvoluted MS/MS spectra with coeluted and background ions from the AIF method, the MS/MS spectrum obtained from the targeted MS/MS approach is cleaner and purer. Therefore, an untargeted metabolomics strategy combining the full scan with the targeted MS/MS method could obtain most discriminatory features along with a high quality MS/MS spectrum for discovering the AD biomarkers.
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Affiliation(s)
- Chih-Wei Chang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, 138 Sheng-Li Road, Tainan 704, Taiwan
| | - Jen-Yi Hsu
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, 138 Sheng-Li Road, Tainan 704, Taiwan
| | - Ping-Zu Hsiao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, 138 Sheng-Li Road, Tainan 704, Taiwan
| | - Yuan-Chih Chen
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, 138 Sheng-Li Road, Tainan 704, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, 138 Sheng-Li Road, Tainan 704, Taiwan
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, 138 Sheng-Li Road, Tainan 704, Taiwan
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Contini C, Serrao S, Manconi B, Olianas A, Iavarone F, Guadalupi G, Messana I, Castagnola M, Masullo C, Bizzarro A, Turck CW, Maccarrone G, Cabras T. Characterization of Cystatin B Interactome in Saliva from Healthy Elderly and Alzheimer’s Disease Patients. Life (Basel) 2023; 13:life13030748. [PMID: 36983903 PMCID: PMC10054399 DOI: 10.3390/life13030748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Cystatin B is a small, multifunctional protein involved in the regulation of inflammation, innate immune response, and neuronal protection and found highly abundant in the brains of patients with Alzheimer’s disease (AD). Recently, our study demonstrated a significant association between the level of salivary cystatin B and AD. Since the protein is able to establish protein-protein interaction (PPI) in different contexts and aggregation-prone proteins and the PPI networks are relevant for AD pathogenesis, and due to the relevance of finding new AD markers in peripheral biofluids, we thought it was interesting to study the possible involvement of cystatin B in PPIs in saliva and to evaluate differences and similarities between AD and age-matched elderly healthy controls (HC). For this purpose, we applied a co-immunoprecipitation procedure and a bottom-up proteomics analysis to purify, identify, and quantify cystatin B interactors. Results demonstrated for the first time the existence of a salivary cystatin B-linked multi-protein complex composed by 82 interactors and largely expressed in the body. Interactors are involved in neutrophil activation, antimicrobial activity, modulation of the cytoskeleton and extra-cellular matrix (ECM), and glucose metabolism. Preliminary quantitative data showed significantly lower levels of triosophosphate isomerase 1 and higher levels of mucin 7, BPI, and matrix Gla protein in AD with respect to HC, suggesting implications associated with AD of altered glucose metabolism, antibacterial activities, and calcification-associated processes. Data are available via ProteomeXchange with identifiers PXD039286 and PXD030679.
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Affiliation(s)
- Cristina Contini
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Simone Serrao
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Barbara Manconi
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
- Correspondence:
| | - Alessandra Olianas
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Federica Iavarone
- Department of Basic Biotechnological Sciences, Intensive and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Policlinico Universitario “A. Gemelli” Foundation IRCCS, 00168 Rome, Italy
| | - Giulia Guadalupi
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Irene Messana
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Consiglio Nazionale delle Ricerche, 00168 Rome, Italy
| | - Massimo Castagnola
- Proteomics Laboratory, European Center for Brain Research, (IRCCS) Santa Lucia Foundation, 00168 Rome, Italy
| | - Carlo Masullo
- Department of Neuroscience, Neurology Section, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | | | - Christoph W. Turck
- Proteomics and Biomarkers, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Giuseppina Maccarrone
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Tiziana Cabras
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
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Hyvärinen E, Solje E, Vepsäläinen J, Kullaa A, Tynkkynen T. Salivary Metabolomics in the Diagnosis and Monitoring of Neurodegenerative Dementia. Metabolites 2023; 13:metabo13020233. [PMID: 36837852 PMCID: PMC9968225 DOI: 10.3390/metabo13020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/17/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Millions of people suffer with dementia worldwide. However, early diagnosis of neurodegenerative diseases/dementia (NDD) is difficult, and no specific biomarkers have been found. This study aims to review the applications of salivary metabolomics in diagnostics and the treatment monitoring of NDD A literature search of suitable studies was executed so that a total of 29 original research articles were included in the present review. Spectroscopic methods, mainly nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry, give us a broad view of changes in salivary metabolites in neurodegenerative diseases. The role of different salivary metabolites in brain function is discussed. Further studies with larger patient cohorts should be carried out to investigate the association between salivary metabolites and brain function and thus learn more about the complicated pathways in the human body.
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Affiliation(s)
- Eelis Hyvärinen
- Institute of Dentistry, University of Eastern Finland, 70210 Kuopio, Finland
| | - Eino Solje
- Institute of Clinical Medicine, Neurology, University of Eastern Finland, 70210 Kuopio, Finland
- Neuro Center, Neurology, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Jouko Vepsäläinen
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, 70210 Kuopio, Finland
| | - Arja Kullaa
- Institute of Dentistry, University of Eastern Finland, 70210 Kuopio, Finland
- Correspondence: ; Tel.: +358-44-515-0452
| | - Tuulia Tynkkynen
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, 70210 Kuopio, Finland
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Yang Y, Lv J, Bai H, Ren L, Yang J, Ding Y, Liu C, Chen X. Periodontal Status and Saliva Metabolic Signature in Patients with Alzheimer's Disease. J Alzheimers Dis 2023; 95:603-613. [PMID: 37424468 DOI: 10.3233/jad-230291] [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: 07/11/2023]
Abstract
BACKGROUND Characterizing the periodontal status of patients with Alzheimer's disease (AD), investigating differences in salivary metabolism between patients with and without AD under the same periodontal conditions, and understanding how it is related to oral flora are critical. OBJECTIVE We aimed to examine the periodontal condition of patients with AD and to screen salivary metabolic biomarkers from the saliva of individuals with and without AD with matched periodontal conditions. Furthermore, we aimed to explore the possible relationship between salivary metabolic changes and oral flora. METHODS In total, 79 individuals were recruited into the experiment for periodontal analysis. Especially, 30 saliva samples from the AD group and 30 from healthy controls (HCs) with matched periodontal conditions were selected for metabolomic analysis. The random-forest algorithm was used to detect candidate biomarkers. Among these, 19 AD saliva and 19 HC samples were selected to investigate the microbiological factors influencing the alterations in saliva metabolism in patients with AD. RESULTS The plaque index and bleeding on probing were considerably higher in the AD group. Further, Cis-3-(1-carboxy-ethyl)-3,5-cyclohexadiene-1,2-diol, dodecanoic acid, genipic acid, and N, N-dimethylthanolamine N-oxide were determined as candidate biomarkers, based on the area under the curve (AUC) value (AUC = 0.95). The results of oral-flora sequencing showed that dysbacteriosis may be a reason for the differences in AD saliva metabolism. CONCLUSION Dysregulation of the proportion of specific bacterial flora in saliva plays a vital role in metabolic changes in AD. These results will contribute to further improving the AD saliva biomarker system.
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Affiliation(s)
- Yi Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jiaxi Lv
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Huimin Bai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Liang Ren
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jing Yang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yi Ding
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xueping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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McNicholas K, François M, Liu JW, Doecke JD, Hecker J, Faunt J, Maddison J, Johns S, Pukala TL, Rush RA, Leifert WR. Salivary inflammatory biomarkers are predictive of mild cognitive impairment and Alzheimer's disease in a feasibility study. Front Aging Neurosci 2022; 14:1019296. [PMID: 36438010 PMCID: PMC9685799 DOI: 10.3389/fnagi.2022.1019296] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/26/2022] [Indexed: 09/10/2023] Open
Abstract
Alzheimer's disease (AD) is an insidious disease. Its distinctive pathology forms over a considerable length of time without symptoms. There is a need to detect this disease, before even subtle changes occur in cognition. Hallmark AD biomarkers, tau and amyloid-β, have shown promising results in CSF and blood. However, detecting early changes in these biomarkers and others will involve screening a wide group of healthy, asymptomatic individuals. Saliva is a feasible alternative. Sample collection is economical, non-invasive and saliva is an abundant source of proteins including tau and amyloid-β. This work sought to extend an earlier promising untargeted mass spectrometry study in saliva from individuals with mild cognitive impairment (MCI) or AD with age- and gender-matched cognitively normal from the South Australian Neurodegenerative Disease cohort. Five proteins, with key roles in inflammation, were chosen from this study and measured by ELISA from individuals with AD (n = 16), MCI (n = 15) and cognitively normal (n = 29). The concentrations of Cystatin-C, Interleukin-1 receptor antagonist, Stratifin, Matrix metalloproteinase 9 and Haptoglobin proteins had altered abundance in saliva from AD and MCI, consistent with the earlier study. Receiver operating characteristic analysis showed that combinations of these proteins demonstrated excellent diagnostic accuracy for distinguishing both MCI (area under curve = 0.97) and AD (area under curve = 0.97) from cognitively normal. These results provide evidence for saliva being a valuable source of biomarkers for early detection of cognitive impairment in individuals on the AD continuum and potentially other neurodegenerative diseases.
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Affiliation(s)
- Kym McNicholas
- Molecular Diagnostic Solutions Group, Human Health Program, CSIRO Health and Biosecurity, Adelaide, SA, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Maxime François
- Molecular Diagnostic Solutions Group, Human Health Program, CSIRO Health and Biosecurity, Adelaide, SA, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Jian-Wei Liu
- CSIRO Land and Water, Black Mountain Research and Innovation Park, Canberra, ACT, Australia
| | - James D. Doecke
- Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Jane Hecker
- Department of Internal Medicine, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Jeff Faunt
- Department of General Medicine, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - John Maddison
- Aged Care Rehabilitation and Palliative Care, SA Health, Modbury Hospital, Modbury, SA, Australia
| | - Sally Johns
- Aged Care Rehabilitation and Palliative Care, SA Health, Modbury Hospital, Modbury, SA, Australia
| | - Tara L. Pukala
- School of Physical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | | | - Wayne R. Leifert
- Molecular Diagnostic Solutions Group, Human Health Program, CSIRO Health and Biosecurity, Adelaide, SA, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
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10
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Shrode RL, Cady N, Jensen SN, Borcherding N, Mangalam AK. Isoflavone consumption reduces inflammation through modulation of phenylalanine and lipid metabolism. Metabolomics 2022; 18:84. [PMID: 36289122 PMCID: PMC10148689 DOI: 10.1007/s11306-022-01944-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/11/2022] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Phytoestrogens found in soy, fruits, peanuts, and other legumes, have been identified as metabolites capable of providing beneficial effects in multiple pathological conditions due to their ability to mimic endogenous estrogen. Interestingly, the health-promoting effects of some phytoestrogens, such as isoflavones, are dependent on the presence of specific gut bacteria. Specifically, gut bacteria can metabolize isoflavones into equol, which has a higher affinity for endogenous estrogen receptors compared to dietary isoflavones. We have previously shown that patients with multiple sclerosis (MS), a neuroinflammatory disease, lack gut bacteria that are able to metabolize phytoestrogen. Further, we have validated the importance of both isoflavones and phytoestrogen-metabolizing gut bacteria in disease protection utilizing an animal model of MS. Specifically, we have shown that an isoflavone-rich diet can protect from neuroinflammatory diseases, and that protection was dependent on the ability of gut bacteria to metabolize isoflavones into equol. Additionally, mice on a diet with isoflavones showed an anti-inflammatory response compared to the mice on a diet lacking isoflavones. However, it is unknown how isoflavones and/or equol mediates their protective effects, especially their effects on host metabolite levels. OBJECTIVES In this study, we utilized untargeted metabolomics to identify metabolites found in plasma that were modulated by the presence of dietary isoflavones. RESULTS We found that the consumption of isoflavones increased anti-inflammatory monounsaturated fatty acids and beneficial polyunsaturated fatty acids while reducing pro-inflammatory glycerophospholipids, sphingolipids, phenylalanine metabolism, and arachidonic acid derivatives. CONCLUSION Isoflavone consumption alters the systemic metabolic landscape through concurrent increases in monounsaturated fatty acids and beneficial polyunsaturated fatty acids plus reduction in pro-inflammatory metabolites and pathways. This highlights a potential mechanism by which an isoflavone diet may modulate immune-mediated disease.
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Affiliation(s)
- Rachel L Shrode
- Department of Informatics, University of Iowa, Iowa City, IA, 52242, USA
| | - Nicole Cady
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Samantha N Jensen
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, 52242, USA
- Division of Gastroenterology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Nicholas Borcherding
- Department of Pathology and Immunology, School of Medicine, Washington University, St. Louis, MO, 63110, USA
| | - Ashutosh K Mangalam
- Department of Informatics, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, 52242, USA.
- Iowa Institute for Oral Health Research, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA.
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11
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François M, Karpe AV, Liu JW, Beale DJ, Hor M, Hecker J, Faunt J, Maddison J, Johns S, Doecke JD, Rose S, Leifert WR. Multi-Omics, an Integrated Approach to Identify Novel Blood Biomarkers of Alzheimer's Disease. Metabolites 2022; 12:949. [PMID: 36295851 PMCID: PMC9610280 DOI: 10.3390/metabo12100949] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022] Open
Abstract
The metabolomic and proteomic basis of mild cognitive impairment (MCI) and Alzheimer's disease (AD) is poorly understood, and the relationships between systemic abnormalities in metabolism and AD/MCI pathogenesis is unclear. This study compared the metabolomic and proteomic signature of plasma from cognitively normal (CN) and dementia patients diagnosed with MCI or AD, to identify specific cellular pathways and new biomarkers altered with the progression of the disease. We analysed 80 plasma samples from individuals with MCI or AD, as well as age- and gender-matched CN individuals, by utilising mass spectrometry methods and data analyses that included combined pathway analysis and model predictions. Several proteins clearly identified AD from the MCI and CN groups and included plasma actins, mannan-binding lectin serine protease 1, serum amyloid A2, fibronectin and extracellular matrix protein 1 and Keratin 9. The integrated pathway analysis showed various metabolic pathways were affected in AD, such as the arginine, alanine, aspartate, glutamate and pyruvate metabolism pathways. Therefore, our multi-omics approach identified novel plasma biomarkers for the MCI and AD groups, identified changes in metabolic processes, and may form the basis of a biomarker panel for stratifying dementia participants in future clinical trials.
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Affiliation(s)
- Maxime François
- CSIRO Health & Biosecurity, Human Health Program, Molecular Diagnostic Solutions Group, Adelaide, SA 5000, Australia
| | - Avinash V. Karpe
- CSIRO Land & Water, Metabolomics Unit, Ecosciences Precinct, Dutton Park, QLD 4001, Australia
| | - Jian-Wei Liu
- CSIRO Land & Water, Agricultural and Environmental Sciences Precinct, Acton, Canberra, ACT 2601, Australia
| | - David J. Beale
- CSIRO Land & Water, Metabolomics Unit, Ecosciences Precinct, Dutton Park, QLD 4001, Australia
| | - Maryam Hor
- CSIRO Health & Biosecurity, Human Health Program, Molecular Diagnostic Solutions Group, Adelaide, SA 5000, Australia
| | - Jane Hecker
- Department of Internal Medicine, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Jeff Faunt
- Department of General Medicine, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - John Maddison
- Aged Care Rehabilitation & Palliative Care, SA Health, Modbury Hospital, Modbury, SA 5092, Australia
| | - Sally Johns
- Aged Care Rehabilitation & Palliative Care, SA Health, Modbury Hospital, Modbury, SA 5092, Australia
| | - James D. Doecke
- Australian e-Health Research Centre, CSIRO, Level 7, Surgical Treatment and Rehabilitation Service—STARS, Herston, QLD 4029, Australia
| | - Stephen Rose
- Australian e-Health Research Centre, CSIRO, Level 7, Surgical Treatment and Rehabilitation Service—STARS, Herston, QLD 4029, Australia
| | - Wayne R. Leifert
- CSIRO Health & Biosecurity, Human Health Program, Molecular Diagnostic Solutions Group, Adelaide, SA 5000, Australia
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12
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Gong X, Zhang H, Liu X, Liu Y, Liu J, Fapohunda FO, Lü P, Wang K, Tang M. Is liquid biopsy mature enough for the diagnosis of Alzheimer's disease? Front Aging Neurosci 2022; 14:977999. [PMID: 35992602 PMCID: PMC9389010 DOI: 10.3389/fnagi.2022.977999] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 07/18/2022] [Indexed: 01/10/2023] Open
Abstract
The preclinical diagnosis and clinical practice for Alzheimer's disease (AD) based on liquid biopsy have made great progress in recent years. As liquid biopsy is a fast, low-cost, and easy way to get the phase of AD, continual efforts from intense multidisciplinary studies have been made to move the research tools to routine clinical diagnostics. On one hand, technological breakthroughs have brought new detection methods to the outputs of liquid biopsy to stratify AD cases, resulting in higher accuracy and efficiency of diagnosis. On the other hand, diversiform biofluid biomarkers derived from cerebrospinal fluid (CSF), blood, urine, Saliva, and exosome were screened out and biologically verified. As a result, more detailed knowledge about the molecular pathogenesis of AD was discovered and elucidated. However, to date, how to weigh the reports derived from liquid biopsy for preclinical AD diagnosis is an ongoing question. In this review, we briefly introduce liquid biopsy and the role it plays in research and clinical practice. Then, we summarize the established fluid-based assays of the current state for AD diagnostic such as ELISA, single-molecule array (Simoa), Immunoprecipitation-Mass Spectrometry (IP-MS), liquid chromatography-MS, immunomagnetic reduction (IMR), multimer detection system (MDS). In addition, we give an updated list of fluid biomarkers in the AD research field. Lastly, the current outstanding challenges and the feasibility to use a stand-alone biomarker in the joint diagnostic strategy are discussed.
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Affiliation(s)
- Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | | | - Peng Lü
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Kun Wang
- Children’s Center, The Affiliated Taian City Central Hospital of Qingdao University, Taian, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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13
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Contini C, Serrao S, Manconi B, Olianas A, Iavarone F, Bizzarro A, Masullo C, Castagnola M, Messana I, Diaz G, Cabras T. Salivary Proteomics Reveals Significant Changes in Relation to Alzheimer's Disease and Aging. J Alzheimers Dis 2022; 89:605-622. [PMID: 35912740 DOI: 10.3233/jad-220246] [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] [Indexed: 12/13/2022]
Abstract
BACKGROUND Aging is a risk factor for several pathologies as Alzheimer's disease (AD). Great interest exists, therefore, in discovering diagnostic biomarkers and indicators discriminating biological aging and health status. To this aim, omic investigations of biological matrices, as saliva, whose sampling is easy and non-invasive, offer great potential. OBJECTIVE Investigate the salivary proteome through a statistical comparison of the proteomic data by several approaches to highlight quali-/quantitative variations associated specifically either to aging or to AD occurrence, and, thus, able to classify the subjects. METHODS Salivary proteomic data of healthy controls under-70 (adults) and over-70 (elderly) years old, and over-70 AD patients, obtained by liquid chromatography/mass spectrometry, were analyzed by multiple Mann-Whitney test, Kendall correlation, and Random-Forest (RF) analysis. RESULTS Almost all the investigated proteins/peptides significantly decreased in relation to aging in elderly subjects, with or without AD, in comparison with adults. AD subjects exhibited the highest levels of α-defensins, thymosin β4, cystatin B, S100A8 and A9. Correlation tests also highlighted age/disease associated differences. RF analysis individuated quali-/quantitative variations in 20 components, as oxidized S100A8 and S100A9, α-defensin 3, P-B peptide, able to classify with great accuracy the subjects into the three groups. CONCLUSION The findings demonstrated a strong change of the salivary protein profile in relation to the aging. Potential biomarkers candidates of AD were individuated in peptides/proteins involved in antimicrobial defense, innate immune system, inflammation, and in oxidative stress. RF analysis revealed the feasibility of the salivary proteome to discriminate groups of subjects based on age and health status.
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Affiliation(s)
- Cristina Contini
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Simone Serrao
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Barbara Manconi
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Alessandra Olianas
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Federica Iavarone
- Department of Basic Biotechnological Sciences, Intensive and Perioperative Clinics, Catholic University of the Sacred Heart, Rome, Italy.,Policlinico Universitario "A. Gemelli" Foundation -IRCCS, Rome, Italy
| | | | - Carlo Masullo
- Department of Neuroscience, Section Neurology, Catholic University of the Sacred Heart, Rome, Italy
| | - Massimo Castagnola
- Proteomics laboratory, European Centre for Research on the Brain, "Santa Lucia" Foundation -IRCCS, Rome, Italy
| | - Irene Messana
- Institute of Chemical Sciences and Technologies "Giulio Natta", National Research Council, Rome, Italy
| | - Giacomo Diaz
- Department of Biomedical Sciences University of Cagliari Cagliari, Italy
| | - Tiziana Cabras
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
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14
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Karpe AV, Liu JW, Shah A, Koloski N, Holtmann G, Beale DJ. Utilising lipid and, arginine and proline metabolism in blood plasma to differentiate the biochemical expression in functional dyspepsia (FD) and irritable bowel syndrome (IBS). Metabolomics 2022; 18:38. [PMID: 35687195 DOI: 10.1007/s11306-022-01900-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/25/2022] [Indexed: 02/07/2023]
Abstract
Functional gastrointestinal disorders (FGID) such as functional dyspepsia (FD) and irritable bowel syndrome (IBS) are highly prevalent and debilitating attributed to altered gut function and gut-brain interactions. FGID can be reliably diagnosed based upon the symptom pattern; but in the clinical setting FD or IBS a frequent diagnoses of exclusion after relevant structural causes of symptoms have been ruled out by appropriate testing. Thus far, there is no established biomarker for FGIDs. To address this limitation, we utilised multi-omics and chemometrics integration to characterise the blood plasma biochemistry in patients with IBS, FD, an overlap of FD/IBS, and controls using liquid chromatography-mass spectrometry (LC-MS) techniques.Cholesterol metabolism products Cholest-5,24-dien-3β-ol, 3-O-β-D-glucopyranoside, energy pathway metabolites, immunoglobulin-γ2 and immunoglobulin-κ, and carbonic anhydrase-1 proteins were particularly elevated in IBS. Furthermore, arginine and proline metabolisms, thyroid hormone synthesis, ferroptosis and, complementary and coagulation cascades were particularly upregulated in patients with IBS. Cer(d18:1/26:1(17Z)) and PI(14:0/22:1(11Z)) lipids were elevated in FD and FD-IBS but were depleted in IBS. Markers of central carbon metabolism and lipidome profiles allowed better discrimination and model predictability than metaproteome profile in healthy and FGID conditions.Overall, the multi-omics integration allowed the discrimination of healthy controls and FGID patients. It also effectively differentiated the biochemistry of FGID subtypes including FD, IBS and FD-IBS co-occurrence. This study points towards the possibility of multi-omics integration for rapid and high throughput analysis of plasma samples to support clinicians screen and diagnose patients with suspected FGIDs.
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Affiliation(s)
- Avinash V Karpe
- CSIRO Land and Water, P. O. Box 2583, 4001, Dutton Park, QLD, Australia
- Department of Chemistry & Biotechnology, School of Science, Computing & Engineering Technologies (SoSCET), Swinburne University of Technology, 3122, Hawthorn, VIC, Australia
| | - Jian-Wei Liu
- CSIRO Land and Water, Black Mountain, Clunies Ross Street, 2601, Acton, ACT, Australia
| | - Ayesha Shah
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, 4103, Woolloongabba, QLD, Australia
| | - Natasha Koloski
- Faculty of Health and Medicine, University of Newcastle, 2308, Callaghan, NSW, Australia
- School of Medicine, The University of Queensland, 4072, St. Lucia, QLD, Australia
| | - Gerald Holtmann
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, 4103, Woolloongabba, QLD, Australia
- School of Medicine, The University of Queensland, 4072, St. Lucia, QLD, Australia
| | - David J Beale
- CSIRO Land and Water, P. O. Box 2583, 4001, Dutton Park, QLD, Australia.
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