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Maru K, Singh A, Jangir R, Jangir KK. Amyloid detection in neurodegenerative diseases using MOFs. J Mater Chem B 2024; 12:4553-4573. [PMID: 38646795 DOI: 10.1039/d4tb00373j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Neurodegenerative diseases (amyloid diseases such as Alzheimer's and Parkinson's), stemming from protein misfolding and aggregation, encompass a spectrum of disorders with severe systemic implications. Timely detection is pivotal in managing these diseases owing to their significant impact on organ function and high mortality rates. The diverse array of amyloid disorders, spanning localized and systemic manifestations, underscores the complexity of these conditions and highlights the need for advanced detection methods. Traditional approaches have focused on identifying biomarkers using imaging techniques (PET and MRI) or invasive procedures. However, recent efforts have focused on the use of metal-organic frameworks (MOFs), a versatile class of materials known for their unique properties, in revolutionizing amyloid disease detection. The high porosity, customizable structures, and biocompatibility of MOFs enable their integration with biomolecules, laying the groundwork for highly sensitive and specific biosensors. These sensors have been employed using electrochemical and photophysical techniques that target amyloid species under neurodegenerative conditions. The adaptability of MOFs allows for the precise detection and quantification of amyloid proteins, offering potential advancements in early diagnosis and disease management. This review article delves into how MOFs contribute to detecting amyloid diseases by categorizing their uses based on different sensing methods, such as electrochemical (EC), electrochemiluminescence (ECL), fluorescence, Förster resonance energy transfer (FRET), up-conversion luminescence resonance energy transfer (ULRET), and photoelectrochemical (PEC) sensing. The drawbacks of MOF biosensors and the challenges encountered in the field are also briefly explored from our perspective.
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Affiliation(s)
- Ketan Maru
- Sardar Vallabhbhai National Institute of Technology, Ichchanath, Surat-395 007, Gujarat, India.
| | - Amarendra Singh
- Sardar Vallabhbhai National Institute of Technology, Ichchanath, Surat-395 007, Gujarat, India.
| | - Ritambhara Jangir
- Sardar Vallabhbhai National Institute of Technology, Ichchanath, Surat-395 007, Gujarat, India.
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2
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Guo B, Li QY, Liu XJ, Luo GH, Wu YJ, Nie J. Diabetes mellitus and Alzheimer's disease: Vacuolar adenosine triphosphatase as a potential link. Eur J Neurosci 2024; 59:2577-2595. [PMID: 38419188 DOI: 10.1111/ejn.16286] [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: 12/01/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Globally, the incidence of diabetes mellitus (DM) and Alzheimer's disease (AD) is increasing year by year, causing a huge economic and social burden, and their pathogenesis and aetiology have been proven to have a certain correlation. In recent years, more and more studies have shown that vacuolar adenosine triphosphatases (v-ATPases) in eukaryotes, which are biomolecules regulating lysosomal acidification and glycolipid metabolism, play a key role in DM and AD. This article describes the role of v-ATPase in DM and AD, including its role in glycolysis, insulin secretion and insulin resistance (IR), as well as its relationship with lysosomal acidification, autophagy and β-amyloid (Aβ). In DM, v-ATPase is involved in the regulation of glucose metabolism and IR. v-ATPase is closely related to glycolysis. On the one hand, v-ATPase affects the rate of glycolysis by affecting the secretion of insulin and changing the activities of key glycolytic enzymes hexokinase (HK) and phosphofructokinase 1 (PFK-1). On the other hand, glucose is the main regulator of this enzyme, and the assembly and activity of v-ATPase depend on glucose, and glucose depletion will lead to its decomposition and inactivation. In addition, v-ATPase can also regulate free fatty acids, thereby improving IR. In AD, v-ATPase can not only improve the abnormal brain energy metabolism by affecting lysosomal acidification and autophagy but also change the deposition of Aβ by affecting the production and degradation of Aβ. Therefore, v-ATPase may be the bridge between DM and AD.
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Affiliation(s)
- Bin Guo
- Key Laboratory of Basic Pharmacology of the Ministry of Education and Joint International Research Laboratory of Ethnomedicine of the Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Qi-Ye Li
- Key Laboratory of Basic Pharmacology of the Ministry of Education and Joint International Research Laboratory of Ethnomedicine of the Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xue-Jia Liu
- Key Laboratory of Basic Pharmacology of the Ministry of Education and Joint International Research Laboratory of Ethnomedicine of the Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Guo-Hui Luo
- Key Laboratory of Basic Pharmacology of the Ministry of Education and Joint International Research Laboratory of Ethnomedicine of the Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Ya-Juan Wu
- Key Laboratory of Basic Pharmacology of the Ministry of Education and Joint International Research Laboratory of Ethnomedicine of the Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jing Nie
- Key Laboratory of Basic Pharmacology of the Ministry of Education and Joint International Research Laboratory of Ethnomedicine of the Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
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3
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Angeloni C, Malaguti M, Prata C, Freschi M, Barbalace MC, Hrelia S. Mechanisms Underlying Neurodegenerative Disorders and Potential Neuroprotective Activity of Agrifood By-Products. Antioxidants (Basel) 2022; 12:94. [PMID: 36670956 PMCID: PMC9854890 DOI: 10.3390/antiox12010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 01/03/2023] Open
Abstract
Neurodegenerative diseases, characterized by progressive loss in selected areas of the nervous system, are becoming increasingly prevalent worldwide due to an aging population. Despite their diverse clinical manifestations, neurodegenerative diseases are multifactorial disorders with standard features and mechanisms such as abnormal protein aggregation, mitochondrial dysfunction, oxidative stress and inflammation. As there are no effective treatments to counteract neurodegenerative diseases, increasing interest has been directed to the potential neuroprotective activities of plant-derived compounds found abundantly in food and in agrifood by-products. Food waste has an extremely negative impact on the environment, and recycling is needed to promote their disposal and overcome this problem. Many studies have been carried out to develop green and effective strategies to extract bioactive compounds from food by-products, such as peel, leaves, seeds, bran, kernel, pomace, and oil cake, and to investigate their biological activity. In this review, we focused on the potential neuroprotective activity of agrifood wastes obtained by common products widely produced and consumed in Italy, such as grapes, coffee, tomatoes, olives, chestnuts, onions, apples, and pomegranates.
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Affiliation(s)
- Cristina Angeloni
- Department for Life Quality Studies, Alma Mater Studiorum–University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy
| | - Marco Malaguti
- Department for Life Quality Studies, Alma Mater Studiorum–University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy
| | - Cecilia Prata
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Michela Freschi
- Department for Life Quality Studies, Alma Mater Studiorum–University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy
| | - Maria Cristina Barbalace
- Department for Life Quality Studies, Alma Mater Studiorum–University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy
| | - Silvana Hrelia
- Department for Life Quality Studies, Alma Mater Studiorum–University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy
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4
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Casas-Fernández E, Peña-Bautista C, Baquero M, Cháfer-Pericás C. Lipids as Early and Minimally Invasive Biomarkers for Alzheimer's Disease. Curr Neuropharmacol 2022; 20:1613-1631. [PMID: 34727857 PMCID: PMC9881089 DOI: 10.2174/1570159x19666211102150955] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/09/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder worldwide. Specifically, typical late-onset AD is a sporadic form with a complex etiology that affects over 90% of patients. The current gold standard for AD diagnosis is based on the determination of amyloid status by analyzing cerebrospinal fluid samples or brain positron emission tomography. These procedures can be used widely as they have several disadvantages (expensive, invasive). As an alternative, blood metabolites have recently emerged as promising AD biomarkers. Small molecules that cross the compromised AD blood-brain barrier could be determined in plasma to improve clinical AD diagnosis at early stages through minimally invasive techniques. Specifically, lipids could play an important role in AD since the brain has a high lipid content, and they are present ubiquitously inside amyloid plaques. Therefore, a systematic review was performed with the aim of identifying blood lipid metabolites as potential early AD biomarkers. In conclusion, some lipid families (fatty acids, glycerolipids, glycerophospholipids, sphingolipids, lipid peroxidation compounds) have shown impaired levels at early AD stages. Ceramide levels were significantly higher in AD subjects, and polyunsaturated fatty acids levels were significantly lower in AD. Also, high arachidonic acid levels were found in AD patients in contrast to low sphingomyelin levels. Consequently, these lipid biomarkers could be used for minimally invasive and early AD clinical diagnosis.
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Affiliation(s)
| | | | - Miguel Baquero
- Division of Neurology, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Consuelo Cháfer-Pericás
- Health Research Institute La Fe, Valencia, Spain;,Address correspondence to this author at the Health Research Institute La Fe, Avenida Fernando Abril Martorell 106, Valencia E46026, Spain;, Tel: +34-96 1246721; E-mail:
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5
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Zakharova NV, Kononikhin AS, Indeykina MI, Bugrova AE, Strelnikova P, Pekov S, Kozin SA, Popov IA, Mitkevich V, Makarov AA, Nikolaev EN. Mass spectrometric studies of the variety of beta-amyloid proteoforms in Alzheimer's disease. MASS SPECTROMETRY REVIEWS 2022:e21775. [PMID: 35347731 DOI: 10.1002/mas.21775] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/03/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
This review covers the results of the application of mass spectrometric (MS) techniques to study the diversity of beta-amyloid (Aβ) peptides in human samples. Since Aβ is an important hallmark of Alzheimer's disease (AD), which is a socially significant neurodegenerative disorder of the elderly worldwide, analysis of its endogenous variations is of particular importance for elucidating the pathogenesis of AD, predicting increased risks of the disease onset, and developing effective therapy. MS approaches have no alternative for the study of complex samples, including a wide variety of Aβ proteoforms, differing in length and modifications. Approaches based on matrix-assisted laser desorption/ionization time-of-flight and liquid chromatography with electrospray ionization tandem MS are most common in Aβ studies. However, Aβ forms with isomerized and/or racemized Asp and Ser residues require the use of special methods for separation and extra sensitive and selective methods for detection. Overall, this review summarizes current knowledge of Aβ species found in human brain, cerebrospinal fluid, and blood plasma; focuses on application of different MS approaches for Aβ studies; and considers the potential of MS techniques for further studies of Aβ-peptides.
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Affiliation(s)
- Natalia V Zakharova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Kononikhin
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria I Indeykina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna E Bugrova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Polina Strelnikova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Stanislav Pekov
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Igor A Popov
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- N.N. Semenov Federal Center of Chemical Physics, V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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6
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Changes in the Cerebrospinal Fluid and Plasma Lipidome in Patients with Rett Syndrome. Metabolites 2022; 12:metabo12040291. [PMID: 35448478 PMCID: PMC9026385 DOI: 10.3390/metabo12040291] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023] Open
Abstract
Rett syndrome (RTT) is defined as a rare disease caused by mutations of the methyl-CpG binding protein 2 (MECP2). It is one of the most common causes of genetic mental retardation in girls, characterized by normal early psychomotor development, followed by severe neurologic regression. Hitherto, RTT lacks a specific biomarker, but altered lipid homeostasis has been found in RTT model mice as well as in RTT patients. We performed LC-MS/MS lipidomics analysis to investigate the cerebrospinal fluid (CSF) and plasma composition of patients with RTT for biochemical variations compared to healthy controls. In all seven RTT patients, we found decreased CSF cholesterol levels compared to age-matched controls (n = 13), whereas plasma cholesterol levels were within the normal range in all 13 RTT patients compared to 18 controls. Levels of phospholipid (PL) and sphingomyelin (SM) species were decreased in CSF of RTT patients, whereas the lipidomics profile of plasma samples was unaltered in RTT patients compared to healthy controls. This study shows that the CSF lipidomics profile is altered in RTT, which is the basis for future (functional) studies to validate selected lipid species as CSF biomarkers for RTT.
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7
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Wacławczyk D, Silberring J, Grasso G. The insulin-degrading enzyme as a link between insulin and neuropeptides metabolism. J Enzyme Inhib Med Chem 2021; 36:183-187. [PMID: 33401948 PMCID: PMC7801110 DOI: 10.1080/14756366.2020.1850712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 10/28/2022] Open
Abstract
We have applied a recently developed HPLC-MS enzymatic assay to investigate the cryptic peptides generated by the action of the insulin-degrading enzyme (IDE) on some neuropeptides (NPs) involved in the development of tolerance and dependence to opioids. Particularly, the tested NPs are generated from the NPFF precursor (pro-NPFF (A)): NPFF (FLFQPQRF) and NPAF (AGEGLSSPFWSLAAPQRF). The results show that IDE is able to cleave NPFF and NPAF, generating specific cryptic peptides. As IDE is also responsible for the processing of many other peptides in the brain (amyloid beta protein among the others), we have also performed competitive degradation assays using mixtures of insulin and the above mentioned NPs. Data show that insulin is able to slow down the degradation of both NPs tested, whereas, surprisingly, NPAF is able to accelerate insulin degradation, hinting IDE as the possible link responsible of the mutual influence between insulin and NPs metabolism.
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Affiliation(s)
- Dorota Wacławczyk
- Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Krakow, Poland
| | - Jerzy Silberring
- Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Krakow, Poland
| | - Giuseppe Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
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8
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Michno W, Blennow K, Zetterberg H, Brinkmalm G. Refining the amyloid β peptide and oligomer fingerprint ambiguities in Alzheimer's disease: Mass spectrometric molecular characterization in brain, cerebrospinal fluid, blood, and plasma. J Neurochem 2021; 159:234-257. [PMID: 34245565 DOI: 10.1111/jnc.15466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/11/2021] [Accepted: 07/06/2021] [Indexed: 01/05/2023]
Abstract
Since its discovery, amyloid-β (Aβ) has been the principal target of investigation of in Alzheimer's disease (AD). Over the years however, no clear correlation was found between the Aβ plaque burden and location, and AD-associated neurodegeneration and cognitive decline. Instead, diagnostic potential of specific Aβ peptides and/or their ratio, was established. For instance, a selective reduction in the concentration of the aggregation-prone 42 amino acid-long Aβ peptide (Aβ42) in cerebrospinal fluid (CSF) was put forward as reflective of Aβ peptide aggregation in the brain. With time, Aβ oligomers-the proposed toxic Aβ intermediates-have emerged as potential drivers of synaptic dysfunction and neurodegeneration in the disease process. Oligomers are commonly agreed upon to come in different shapes and sizes, and are very poorly characterized when it comes to their composition and their "toxic" properties. The concept of structural polymorphism-a diversity in conformational organization of amyloid aggregates-that depends on the Aβ peptide backbone, makes the characterization of Aβ aggregates and their role in AD progression challenging. In this review, we revisit the history of Aβ discovery and initial characterization and highlight the crucial role mass spectrometry (MS) has played in this process. We critically review the common knowledge gaps in the molecular identity of the Aβ peptide, and how MS is aiding the characterization of higher order Aβ assemblies. Finally, we go on to present recent advances in MS approaches for characterization of Aβ as single peptides and oligomers, and convey our optimism, as to how MS holds a promise for paving the way for progress toward a more comprehensive understanding of Aβ in AD research.
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Affiliation(s)
- Wojciech Michno
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK.,Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Gunnar Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
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9
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Ai Y, Zhao P, FNU PIJ, Chen H. Absolute Quantitation of Tryptophan-Containing Peptides and Amyloid β-Peptide Fragments by Coulometric Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1771-1779. [PMID: 34101439 PMCID: PMC8925997 DOI: 10.1021/jasms.1c00121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Isotope-labeled internal standards are routinely used for mass spectrometry (MS)-based absolute quantitation. However, syntheses of isotope-labeled peptides are time-consuming and costly. To tackle this issue, we recently developed a coulometric mass spectrometric (CMS) approach for absolute quantitation without the use of standards, based on the electrochemical oxidation of cysteine or tyrosine-containing peptides followed by mass spectrometric measurement of the oxidation yield. To further expand the utility of this method, herein we present the CMS method for absolute quantitation of peptides based on tryptophan electrochemical oxidation. Several tryptophan-containing peptides, such as WGG, WQPPRARI, WAGGDASGE, RTRPLWVRME, and KVPRNQDWL, were successfully quantified with a quantification error ranging from -4.5 to +4.3%. Furthermore, this quantitation approach is also applicable to protein, in which protein can be digested and a surrogate peptide can be selected for quantification to reflect the amount of the parent protein, as exemplified by CMS analysis of peptide GITWK from cytochrome c. The CMS result agreed well with the traditional isotope dilution method, with only a small difference of 3.5%. In addition, CMS was used to successfully quantify amyloid beta (Aβ) peptide fragments (up to 28 amino acid residues) based on tyrosine oxidation. The validity of the CMS method for peptide and protein absolute quantitation without using isotope-labeled peptide standards would greatly facilitate proteomics research.
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Affiliation(s)
| | | | | | - Hao Chen
- Corresponding Author: Hao Chen - Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA 07102
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10
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Fulcher JM, Makaju A, Moore RJ, Zhou M, Bennett DA, De Jager PL, Qian WJ, Paša-Tolić L, Petyuk VA. Enhancing Top-Down Proteomics of Brain Tissue with FAIMS. J Proteome Res 2021; 20:2780-2795. [PMID: 33856812 PMCID: PMC8672206 DOI: 10.1021/acs.jproteome.1c00049] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Proteomic investigations of Alzheimer's and Parkinson's disease have provided valuable insights into neurodegenerative disorders. Thus far, these investigations have largely been restricted to bottom-up approaches, hindering the degree to which one can characterize a protein's "intact" state. Top-down proteomics (TDP) overcomes this limitation; however, it is typically limited to observing only the most abundant proteoforms and of a relatively small size. Therefore, fractionation techniques are commonly used to reduce sample complexity. Here, we investigate gas-phase fractionation through high-field asymmetric waveform ion mobility spectrometry (FAIMS) within TDP. Utilizing a high complexity sample derived from Alzheimer's disease (AD) brain tissue, we describe how the addition of FAIMS to TDP can robustly improve the depth of proteome coverage. For example, implementation of FAIMS with external compensation voltage (CV) stepping at -50, -40, and -30 CV could more than double the mean number of non-redundant proteoforms, genes, and proteome sequence coverage compared to without FAIMS. We also found that FAIMS can influence the transmission of proteoforms and their charge envelopes based on their size. Importantly, FAIMS enabled the identification of intact amyloid beta (Aβ) proteoforms, including the aggregation-prone Aβ1-42 variant which is strongly linked to AD. Raw data and associated files have been deposited to the ProteomeXchange Consortium via the MassIVE data repository with data set identifier PXD023607.
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Affiliation(s)
- James M Fulcher
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Aman Makaju
- Life Sciences Mass Spectrometry Unit, Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Philip L De Jager
- Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Medical Center, New York, New York 10032, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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11
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Navas-Carrillo D, Rivera-Caravaca JM, Sampedro-Andrada A, Orenes-Piñero E. Novel biomarkers in Alzheimer's disease using high resolution proteomics and metabolomics: miRNAS, proteins and metabolites. Crit Rev Clin Lab Sci 2020; 58:167-179. [PMID: 33137264 DOI: 10.1080/10408363.2020.1833298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia. It affects approximately 6% of people over the age of 65 years. It is a clinicopathological, degenerative, chronical and progressive disease that exhibits a deterioration of memory, orientation, speech and other functions. Factors contributing to the pathogenesis of the disease are the presence of extracellular amyloid deposits, called neuritic senile plaques, and fibrillary protein deposits inside neurons, known as neurofibrillary bundles, that appear mainly in the frontal and temporal lobes. AD has a long preclinical latency and is difficult to diagnose and prevent at early stages. Despite the advent of novel high-throughput technologies, it is a great challenge to identify precise biomarkers to understand the progression of the disease and the development of new treatments. In this sense, important knowledge is emerging regarding novel molecular and biological candidates with diagnostic potential, including microRNAs that have a key role in gene repression. On the other hand, proteomic approaches offer a platform for the comprehensive analysis of the whole proteome in a certain physiological time. Proteomic technology investigates protein expression directly and reveals post-translational modifications known to be determinant for many human diseases. Clinically, there is growing evidence for the role of proteomic and metabolomic technologies in AD biomarker discovery. This review discusses the role of several miRNAs identified using genomic technologies, and the importance of novel proteomic and metabolomic approaches to identify new proteins and metabolites that may be useful as biomarkers for monitoring the progression and treatment of AD.
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Affiliation(s)
| | | | | | - Esteban Orenes-Piñero
- Proteomic Unit, Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca (IMIB-Arrixaca), Universidad de Murcia, Murcia, Spain
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12
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Van Thanh Nguyen N, Taverna M, Smadja C, Mai TD. Recent Electrokinetic and Microfluidic Strategies for Detection of Amyloid Beta Peptide Biomarkers: Towards Molecular Diagnosis of Alzheimer's Disease. CHEM REC 2020; 21:149-161. [PMID: 33112020 DOI: 10.1002/tcr.202000103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/05/2020] [Indexed: 11/06/2022]
Abstract
Among all neurodegenerative diseases, Alzheimer's Disease (AD) is the most prevalent worldwide, with a huge burden to the society and no efficient AD treatment so far. Continued efforts have been being made towards early and powerful diagnosis of AD, in the hope for a successful set of clinical trials and subsequently AD curative treatment. Towards this aim, detection and quantification of amyloid beta (Aβ) peptides in cerebrospinal fluid (CSF) and other biofluids, which are established and validated biomarkers for AD, have drawn attention of the scientific community and industry over almost two decades. In this work, an overview on our major contributions over 15 years to develop different electrokinetic and microfluidic strategies for Aβ peptides detection and quantification is reported. Accordingly, discussions and viewpoints on instrumental and methodological developments for microscale electrophoresis, microfluidic designs and immuno-enrichment / assays on magnetic beads in microchannels for tracing Aβ peptides in CSF are given in this review.
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Affiliation(s)
- Ngoc Van Thanh Nguyen
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296, Châtenay-Malabry, France
| | - Myriam Taverna
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296, Châtenay-Malabry, France.,Institut Universitaire de France
| | - Claire Smadja
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296, Châtenay-Malabry, France
| | - Thanh Duc Mai
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296, Châtenay-Malabry, France
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13
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Grasso G. THE USE OF MASS SPECTROMETRY TO STUDY ZN-METALLOPROTEASE-SUBSTRATE INTERACTIONS. MASS SPECTROMETRY REVIEWS 2020; 39:574-585. [PMID: 31898821 DOI: 10.1002/mas.21621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
Zinc metalloproteases (ZnMPs) participate in diverse biological reactions, encompassing the synthesis and degradation of all the major metabolites in living organisms. In particular, ZnMPs have been recognized to play a very important role in controlling the concentration level of several peptides and/or proteins whose homeostasis has to be finely regulated for the correct physiology of cells. Dyshomeostasis of aggregation-prone proteins causes pathological conditions and the development of several different diseases. For this reason, in recent years, many analytical approaches have been applied for studying the interaction between ZnMPs and their substrates and how environmental factors can affect enzyme activities. In this scenario, mass spectrometric methods occupy a very important role in elucidating different aspects of ZnMPs-substrates interaction. These range from identification of cleavage sites to quantitation of kinetic parameters. In this work, an overview of all the main achievements regarding the application of mass spectrometric methods to investigating ZnMPs-substrates interactions is presented. A general experimental protocol is also described which may prove useful to the study of similar interactions. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Giuseppe Grasso
- Department of Chemical Sciences, Università degli Studi di Catania, Viale Andrea Doria 6, Catania, 95125, Italy
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14
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De Simone A, Naldi M, Tedesco D, Bartolini M, Davani L, Andrisano V. Advanced analytical methodologies in Alzheimer’s disease drug discovery. J Pharm Biomed Anal 2020; 178:112899. [DOI: 10.1016/j.jpba.2019.112899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 12/13/2022]
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15
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Fang P, Xie J, Sang S, Zhang L, Liu M, Yang L, Xu Y, Yan G, Yao J, Gao X, Qian W, Wang Z, Zhang Y, Yang P, Shen H. Multilayered N-Glycoproteome Profiling Reveals Highly Heterogeneous and Dysregulated Protein N-Glycosylation Related to Alzheimer’s Disease. Anal Chem 2019; 92:867-874. [PMID: 31751117 DOI: 10.1021/acs.analchem.9b03555] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Pan Fang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - JuanJuan Xie
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Shaoming Sang
- Department of Neurology, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science & Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Mingqi Liu
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lujie Yang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yiteng Xu
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Guoquan Yan
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jun Yao
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xing Gao
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wenjing Qian
- Department of Neurology, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science & Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Zhongfeng Wang
- Department of Neurology, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science & Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Yang Zhang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Pengyuan Yang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Department of Chemistry, Fudan University, Shanghai 200433, China
- Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Huali Shen
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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16
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Bergau N, Maul S, Rujescu D, Simm A, Navarrete Santos A. Reduction of Glycolysis Intermediate Concentrations in the Cerebrospinal Fluid of Alzheimer's Disease Patients. Front Neurosci 2019; 13:871. [PMID: 31496932 PMCID: PMC6713159 DOI: 10.3389/fnins.2019.00871] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/02/2019] [Indexed: 12/22/2022] Open
Abstract
The profile of 122 metabolites in the cerebrospinal fluid (CSF) of patients suffering from Alzheimer's disease (AD) and controls was studied. Among the 122 metabolites analyzed, 61 could be detected. Statistically significant differences between the AD and control group were only detected for metabolites of the glycolysis. Thus, accurate quantification of 11 glycolytic metabolites was done. We detected a significant reduction of five of them, namely phosphoenolpyruvate, 2-phosphoglycerate, 3-phosphoglycerate, pyruvate and dihydroxyacetone phosphate in the AD CSF compared to controls. These results correlate with the known reduction of glucose metabolism in the brain of patients with AD and indicate that metabolic analysis of the central carbon metabolism can be a potential tool in AD diagnostic. Although the Receiver operating characteristic (ROC) analyses of the metabolites do not reach the level of the diagnostic informativity of AD biomarkers, the combination of specific glycolysis metabolites with the established biomarkers may lead to an improvement in sensitivity and specificity.
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Affiliation(s)
- Nick Bergau
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Stephan Maul
- Department of Psychiatry, Psychotherapy and Psychosomatics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Dan Rujescu
- Department of Psychiatry, Psychotherapy and Psychosomatics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Andreas Simm
- Center for Basic Medical Research, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.,Clinic for Cardiac Surgery, University Hospital, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Alexander Navarrete Santos
- Center for Basic Medical Research, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.,Clinic for Cardiac Surgery, University Hospital, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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17
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Wang XJ, Ren JL, Zhang AH, Sun H, Yan GL, Han Y, Liu L. Novel applications of mass spectrometry-based metabolomics in herbal medicines and its active ingredients: Current evidence. MASS SPECTROMETRY REVIEWS 2019; 38:380-402. [PMID: 30817039 DOI: 10.1002/mas.21589] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/25/2019] [Indexed: 06/09/2023]
Abstract
Current evidence shows that herbal medicines could be beneficial for the treatment of various diseases. However, the complexities present in chemical compositions of herbal medicines are currently an obstacle for the progression of herbal medicines, which involve unclear bioactive compounds, mechanisms of action, undetermined targets for therapy, non-specific features for drug metabolism, etc. To overcome those issues, metabolomics can be a great to improve and understand herbal medicines from the small-molecule metabolism level. Metabolomics could solve scientific difficulties with herbal medicines from a metabolic perspective, and promote drug discovery and development. In recent years, mass spectrometry-based metabolomics was widely applied for the analysis of herbal constituents in vivo and in vitro. In this review, we highlight the value of mass spectrometry-based metabolomics and metabolism to address the complexity of herbal medicines in systems pharmacology, and to enhance their biomedical value in biomedicine, to shed light on the aid that mass spectrometry-based metabolomics can offer to the investigation of its active ingredients, especially, to link phytochemical analysis with the assessment of pharmacological effect and therapeutic potential. © 2019 Wiley Periodicals, Inc. Mass Spec Rev.
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Affiliation(s)
- Xi-Jun Wang
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plant, Nanning Guangxi, China
| | - Jun-Ling Ren
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
| | - Ai-Hua Zhang
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
| | - Hui Sun
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
| | - Guang-Li Yan
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
| | - Ying Han
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau
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Shen L, Zhao Y, Zhang H, Feng C, Gao Y, Zhao D, Xia S, Hong Q, Iqbal J, Liu XK, Yao F. Advances in Biomarker Studies in Autism Spectrum Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:207-233. [PMID: 30747425 DOI: 10.1007/978-3-030-05542-4_11] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Autism spectrum disorder (ASD) is a neurological and developmental condition that begins early in childhood and lasts throughout life. The epidemiology of ASD is continuously increasing all over the world with huge social and economical burdens. As the etiology of autism is not completely understood, there is still no medication available for the treatment of this disorder. However, some behavioral interventions are available to improve the core and associated symptoms of autism, particularly when initiated at an early stage. Thus, there is an increasing demand for finding biomarkers for ASD. Although diagnostic biomarkers have not yet been established, research efforts have been carried out in neuroimaging and biological analyses including genomics and gene testing, proteomics, metabolomics, transcriptomics, and studies of the immune system, inflammation, and microRNAs. Here, we will review the current progress in these fields and focus on new methods, developments, research strategies, and studies of blood-based biomarkers.
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Affiliation(s)
- Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China.
| | - Yuxi Zhao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Huajie Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Chengyun Feng
- Maternal and Child Health Hospital of Baoan, Shenzhen, People's Republic of China
| | - Yan Gao
- Maternal and Child Health Hospital of Baoan, Shenzhen, People's Republic of China
| | - Danqing Zhao
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, People's Republic of China
| | - Sijian Xia
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Qi Hong
- Maternal and Child Health Hospital of Baoan, Shenzhen, People's Republic of China
| | - Javed Iqbal
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Xu Kun Liu
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Fang Yao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
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