1
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Seki S, Kitaoka Y, Kawata S, Nishiura A, Uchihashi T, Hiraoka SI, Yokota Y, Isomura ET, Kogo M, Tanaka S. Characteristics of Sensory Neuron Dysfunction in Amyotrophic Lateral Sclerosis (ALS): Potential for ALS Therapy. Biomedicines 2023; 11:2967. [PMID: 38001967 PMCID: PMC10669304 DOI: 10.3390/biomedicines11112967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/24/2023] [Accepted: 10/29/2023] [Indexed: 11/26/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disorder characterised by the progressive degeneration of motor neurons, resulting in muscle weakness, paralysis, and, ultimately, death. Presently, no effective treatment for ALS has been established. Although motor neuron dysfunction is a hallmark of ALS, emerging evidence suggests that sensory neurons are also involved in the disease. In clinical research, 30% of patients with ALS had sensory symptoms and abnormal sensory nerve conduction studies in the lower extremities. Peroneal nerve biopsies show histological abnormalities in 90% of the patients. Preclinical research has reported several genetic abnormalities in the sensory neurons of animal models of ALS, as well as in motor neurons. Furthermore, the aggregation of misfolded proteins like TAR DNA-binding protein 43 has been reported in sensory neurons. This review aims to provide a comprehensive description of ALS-related sensory neuron dysfunction, focusing on its clinical changes and underlying mechanisms. Sensory neuron abnormalities in ALS are not limited to somatosensory issues; proprioceptive sensory neurons, such as MesV and DRG neurons, have been reported to form networks with motor neurons and may be involved in motor control. Despite receiving limited attention, sensory neuron abnormalities in ALS hold potential for new therapies targeting proprioceptive sensory neurons.
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Affiliation(s)
- Soju Seki
- Department of Oral and Maxillofacial Surgery, Graduate School of Dentistry, Osaka University, 1-8 Yamadaoka, Suita 565-0871, Osaka, Japan
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2
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Oh S, Jang Y, Na CH. Discovery of Biomarkers for Amyotrophic Lateral Sclerosis from Human Cerebrospinal Fluid Using Mass-Spectrometry-Based Proteomics. Biomedicines 2023; 11:biomedicines11051250. [PMID: 37238921 DOI: 10.3390/biomedicines11051250] [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] [Received: 03/20/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/28/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by the loss of upper and lower motor neurons, which eventually may lead to death. Critical to the mission of developing effective therapies for ALS is the discovery of biomarkers that can illuminate mechanisms of neurodegeneration and have diagnostic, prognostic, or pharmacodynamic value. Here, we merged unbiased discovery-based approaches and targeted quantitative comparative analyses to identify proteins that are altered in cerebrospinal fluid (CSF) from patients with ALS. Mass spectrometry (MS)-based proteomic approaches employing tandem mass tag (TMT) quantification methods from 40 CSF samples comprising 20 patients with ALS and 20 healthy control (HC) individuals identified 53 proteins that are differential between the two groups after CSF fractionation. Notably, these proteins included both previously identified ones, validating our approach, and novel ones that have the potential for expanding biomarker repertoire. The identified proteins were subsequently examined using parallel reaction monitoring (PRM) MS methods on 61 unfractionated CSF samples comprising 30 patients with ALS and 31 HC individuals. Fifteen proteins (APOB, APP, CAMK2A, CHI3L1, CHIT1, CLSTN3, ERAP2, FSTL4, GPNMB, JCHAIN, L1CAM, NPTX2, SERPINA1, SERPINA3, and UCHL1) showed significant differences between ALS and the control. Taken together, this study identified multiple novel proteins that are altered in ALS, providing the foundation for developing new biomarkers for ALS.
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Affiliation(s)
- Sungtaek Oh
- Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70170, USA
| | - Yura Jang
- Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Chan Hyun Na
- Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
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3
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Chen X, Zhou L, Cui C, Sun J. Evolving markers in amyotrophic lateral sclerosis. Adv Clin Chem 2023. [DOI: 10.1016/bs.acc.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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4
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Katzeff JS, Bright F, Phan K, Kril JJ, Ittner LM, Kassiou M, Hodges JR, Piguet O, Kiernan MC, Halliday GM, Kim WS. Biomarker discovery and development for frontotemporal dementia and amyotrophic lateral sclerosis. Brain 2022; 145:1598-1609. [PMID: 35202463 PMCID: PMC9166557 DOI: 10.1093/brain/awac077] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 11/12/2022] Open
Abstract
Frontotemporal dementia refers to a group of neurodegenerative disorders characterized by behaviour and language alterations and focal brain atrophy. Amyotrophic lateral sclerosis is a rapidly progressing neurodegenerative disease characterized by loss of motor neurons resulting in muscle wasting and paralysis. Frontotemporal dementia and amyotrophic lateral sclerosis are considered to exist on a disease spectrum given substantial overlap of genetic and molecular signatures. The predominant genetic abnormality in both frontotemporal dementia and amyotrophic lateral sclerosis is an expanded hexanucleotide repeat sequence in the C9orf72 gene. In terms of brain pathology, abnormal aggregates of TAR-DNA-binding protein-43 are predominantly present in frontotemporal dementia and amyotrophic lateral sclerosis patients. Currently, sensitive and specific diagnostic and disease surveillance biomarkers are lacking for both diseases. This has impeded the capacity to monitor disease progression during life and the development of targeted drug therapies for the two diseases. The purpose of this review is to examine the status of current biofluid biomarker discovery and development in frontotemporal dementia and amyotrophic lateral sclerosis. The major pathogenic proteins implicated in different frontotemporal dementia and amyotrophic lateral sclerosis molecular subtypes and proteins associated with neurodegeneration and the immune system will be discussed. Furthermore, the use of mass spectrometry-based proteomics as an emerging tool to identify new biomarkers in frontotemporal dementia and amyotrophic lateral sclerosis will be summarized.
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Affiliation(s)
- Jared S Katzeff
- The University of Sydney, Brain and Mind Centre, Sydney, NSW, Australia.,The University of Sydney, School of Medical Sciences, Sydney, NSW, Australia
| | - Fiona Bright
- The University of Sydney, School of Medical Sciences, Sydney, NSW, Australia.,Dementia Research Centre and Department of Biomedical Sciences, Macquarie University, Sydney, NSW, Australia
| | - Katherine Phan
- The University of Sydney, Brain and Mind Centre, Sydney, NSW, Australia.,The University of Sydney, School of Medical Sciences, Sydney, NSW, Australia
| | - Jillian J Kril
- The University of Sydney, School of Medical Sciences, Sydney, NSW, Australia.,Dementia Research Centre and Department of Biomedical Sciences, Macquarie University, Sydney, NSW, Australia
| | - Lars M Ittner
- Dementia Research Centre and Department of Biomedical Sciences, Macquarie University, Sydney, NSW, Australia
| | - Michael Kassiou
- The University of Sydney, School of Chemistry, Sydney, NSW, Australia
| | - John R Hodges
- The University of Sydney, Brain and Mind Centre, Sydney, NSW, Australia
| | - Olivier Piguet
- The University of Sydney, Brain and Mind Centre, Sydney, NSW, Australia.,The University of Sydney, School of Psychology, Sydney, NSW, Australia
| | - Matthew C Kiernan
- The University of Sydney, Brain and Mind Centre, Sydney, NSW, Australia.,Institute of Clinical Neurosciences, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Glenda M Halliday
- The University of Sydney, Brain and Mind Centre, Sydney, NSW, Australia.,The University of Sydney, School of Medical Sciences, Sydney, NSW, Australia
| | - Woojin Scott Kim
- The University of Sydney, Brain and Mind Centre, Sydney, NSW, Australia.,The University of Sydney, School of Medical Sciences, Sydney, NSW, Australia
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5
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Wang F, Li S, Cheng KW, Rosencrans WM, Chou TF. The p97 Inhibitor UPCDC-30245 Blocks Endo-Lysosomal Degradation. Pharmaceuticals (Basel) 2022; 15:ph15020204. [PMID: 35215314 PMCID: PMC8880557 DOI: 10.3390/ph15020204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/23/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
The diverse modes of action of small molecule inhibitors provide versatile tools to investigate basic biology and develop therapeutics. However, it remains a challenging task to evaluate their exact mechanisms of action. We identified two classes of inhibitors for the p97 ATPase: ATP competitive and allosteric. We showed that the allosteric p97 inhibitor, UPCDC-30245, does not affect two well-known cellular functions of p97, endoplasmic-reticulum-associated protein degradation and the unfolded protein response pathway; instead, it strongly increases the lipidated form of microtubule-associated proteins 1A/1B light chain 3B (LC3-II), suggesting an alteration of autophagic pathways. To evaluate the molecular mechanism, we performed proteomic analysis of UPCDC-30245 treated cells. Our results revealed that UPCDC-30245 blocks endo-lysosomal degradation by inhibiting the formation of early endosome and reducing the acidity of the lysosome, an effect not observed with the potent p97 inhibitor CB-5083. This unique effect allows us to demonstrate UPCDC-30245 exhibits antiviral effects against coronavirus by blocking viral entry.
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Affiliation(s)
- Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (K.-W.C.); (W.M.R.)
- Correspondence: (F.W.); (T.-F.C.); Tel.: +1 626-395-6772 (T.-F.C.)
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (K.-W.C.); (W.M.R.)
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (K.-W.C.); (W.M.R.)
| | - William M. Rosencrans
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (K.-W.C.); (W.M.R.)
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (K.-W.C.); (W.M.R.)
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
- Correspondence: (F.W.); (T.-F.C.); Tel.: +1 626-395-6772 (T.-F.C.)
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6
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Agrawal I, Tripathi P, Biswas S. Mass Spectrometry Based Protein Biomarkers and Drug Target Discovery and Clinical Diagnosis in Age-Related Progressing Neurodegenerative Diseases. Drug Metab Rev 2022; 54:22-36. [PMID: 35038284 DOI: 10.1080/03602532.2022.2029475] [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: 12/30/2022]
Abstract
Neurodegenerative diseases correspond to overly complex health disorders that are driven by intersecting pathophysiology that are often trapped in vicious cycles of degeneration and cognitive decline. The usual diagnostic route of these diseases is based on postmortem examination that involves identifying pathology that is specific to the disease in the brain. However, in such cases, accurate diagnosis of the specific disease is limited because clinical disease presentations are often complex that do not easily allow to discriminate patient's cognitive, behavioral, and functional impairment profiles. Additionally, an early identification and therapeutic intervention of these diseases is pivotal to slow the progression of neurodegeneration and extend healthy life span. Mass spectrometry-based techniques have proven to be hugely promising in biological sample analysis and discovery of biomarkers including protein and peptide biomarkers for potential drug target discovery. Recent studies on these biomarkers have demonstrated their potential for applications in early diagnostics and identifying therapeutic targets to battle against neurodegenerative diseases. In this review, we have presented principles of mass spectrometry (MS) and the associated workflows in analyzing and imaging biological samples for discovery of biomarkers. We have especially focused on age- related progressing neurodegenerative diseases such as Alzheimer's (AD) and Parkinson's disease (PD), Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FTD) and the related MS-based biomarkers developments for these diseases. Finally, we present a future perspective discussing the potential research directions ahead.
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Affiliation(s)
- Ishita Agrawal
- Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Pallavi Tripathi
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Shyamasri Biswas
- USA Prime Biotech LLC, 1330 NW 6th St., Suite A-2, Gainesville, FL 32601, USA
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7
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Thompson AG, Oeckl P, Feneberg E, Bowser R, Otto M, Fischer R, Kessler B, Turner MR. Advancing mechanistic understanding and biomarker development in amyotrophic lateral sclerosis. Expert Rev Proteomics 2021; 18:977-994. [PMID: 34758687 DOI: 10.1080/14789450.2021.2004890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Proteomic analysis has contributed significantly to the study of the neurodegenerative disease amyotrophic lateral sclerosis (ALS). It has helped to define the pathological change common to nearly all cases, namely intracellular aggregates of phosphorylated TDP-43, shifting the focus of pathogenesis in ALS toward RNA biology. Proteomics has also uniquely underpinned the delineation of disease mechanisms in model systems and has been central to recent advances in human ALS biomarker development. AREAS COVERED The contribution of proteomics to understanding the cellular pathological changes, disease mechanisms, and biomarker development in ALS are covered. EXPERT OPINION Proteomics has delivered unique insights into the pathogenesis of ALS and advanced the goal of objective measurements of disease activity to improve therapeutic trials. Further developments in sensitivity and quantification are expected, with application to the presymptomatic phase of human disease offering the hope of prevention strategies.
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Affiliation(s)
| | - Patrick Oeckl
- Department of Neurology, University of Ulm, Ulm, Germany.,German Center for Neurodegenerative Diseases (Dzne e.V.), Ulm, Germany
| | - Emily Feneberg
- Department of Neurology, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Robert Bowser
- Departments of Neurology and Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany.,Department of Neurology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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8
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Tang J, Fu J, Wang Y, Li B, Li Y, Yang Q, Cui X, Hong J, Li X, Chen Y, Xue W, Zhu F. ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies. Brief Bioinform 2021; 21:621-636. [PMID: 30649171 PMCID: PMC7299298 DOI: 10.1093/bib/bby127] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/19/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022] Open
Abstract
Label-free quantification (LFQ) with a specific and sequentially integrated workflow of acquisition technique, quantification tool and processing method has emerged as the popular technique employed in metaproteomic research to provide a comprehensive landscape of the adaptive response of microbes to external stimuli and their interactions with other organisms or host cells. The performance of a specific LFQ workflow is highly dependent on the studied data. Hence, it is essential to discover the most appropriate one for a specific data set. However, it is challenging to perform such discovery due to the large number of possible workflows and the multifaceted nature of the evaluation criteria. Herein, a web server ANPELA (https://idrblab.org/anpela/) was developed and validated as the first tool enabling performance assessment of whole LFQ workflow (collective assessment by five well-established criteria with distinct underlying theories), and it enabled the identification of the optimal LFQ workflow(s) by a comprehensive performance ranking. ANPELA not only automatically detects the diverse formats of data generated by all quantification tools but also provides the most complete set of processing methods among the available web servers and stand-alone tools. Systematic validation using metaproteomic benchmarks revealed ANPELA's capabilities in 1 discovering well-performing workflow(s), (2) enabling assessment from multiple perspectives and (3) validating LFQ accuracy using spiked proteins. ANPELA has a unique ability to evaluate the performance of whole LFQ workflow and enables the discovery of the optimal LFQs by the comprehensive performance ranking of all 560 workflows. Therefore, it has great potential for applications in metaproteomic and other studies requiring LFQ techniques, as many features are shared among proteomic studies.
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Affiliation(s)
- Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Li
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Yinghong Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Qingxia Yang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Xuejiao Cui
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Jiajun Hong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofeng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Yuzong Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
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Ng Kee Kwong KC, Harbham PK, Selvaraj BT, Gregory JM, Pal S, Hardingham GE, Chandran S, Mehta AR. 40 Years of CSF Toxicity Studies in ALS: What Have We Learnt About ALS Pathophysiology? Front Mol Neurosci 2021; 14:647895. [PMID: 33815058 PMCID: PMC8012723 DOI: 10.3389/fnmol.2021.647895] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/24/2021] [Indexed: 12/11/2022] Open
Abstract
Based on early evidence of in vitro neurotoxicity following exposure to serum derived from patients with amyotrophic lateral sclerosis (ALS), several studies have attempted to explore whether cerebrospinal fluid (CSF) obtained from people with ALS could possess similar properties. Although initial findings proved inconclusive, it is now increasingly recognized that ALS-CSF may exert toxicity both in vitro and in vivo. Nevertheless, the mechanism underlying CSF-induced neurodegeneration remains unclear. This review aims to summarize the 40-year long history of CSF toxicity studies in ALS, while discussing the various mechanisms that have been proposed, including glutamate excitotoxicity, proteotoxicity and oxidative stress. Furthermore, we consider the potential implications of a toxic CSF circulatory system in the pathophysiology of ALS, and also assess its significance in the context of current ALS research.
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Affiliation(s)
| | - Pratap K Harbham
- West Midlands Academic Foundation Programme, University of Birmingham, Birmingham, United Kingdom
| | - Bhuvaneish T Selvaraj
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, United Kingdom.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Jenna M Gregory
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, United Kingdom.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,MRC Edinburgh Brain Bank, Academic Department of Neuropathology, University of Edinburgh, Edinburgh, United Kingdom.,Edinburgh Pathology, University of Edinburgh, Edinburgh, United Kingdom
| | - Suvankar Pal
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, United Kingdom
| | - Giles E Hardingham
- UK Dementia Research Institute at University of Edinburgh, Edinburgh, United Kingdom.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Siddharthan Chandran
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, United Kingdom.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Brain Development and Repair, InStem, Bengaluru, India
| | - Arpan R Mehta
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, United Kingdom.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, United Kingdom.,Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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10
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Zhang X, Yin L, Jia X, Zhang Y, Liu T, Zhang L. iTRAQ-based Quantitative Proteomic Analysis of Dural Tissues Reveals Upregulated Haptoglobin to be a Potential Biomarker of Moyamoya Disease. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164617666191210103652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Moyamoya Disease (MMD) is a rare cerebrovascular disease with a high rate
of disability and mortality. Immune reactions have been implicated in the pathogenesis of MMD, however,
the underlying mechanism is still unclear.
Objective:
To identify proteins related to MMD specially involved in the immunogenesis, we performed
a proteomic study.
Methods:
In this work, dural tissues or plasma from 98 patients with MMD, 17 disease controls without
MMD, and 12 healthy donors were included. Proteomic profiles of dural tissues from 4 MMD and
4 disease controls were analyzed by an isobaric tag for relative and absolute quantitation (iTRAQ)-
based proteomics. The immune-related proteins were explored by bioinformatics and the key MMDrelated
proteins were verified by western blot, multiple reaction monitoring methods, enzyme-linked
immunosorbent assay, and tissue microarray.
Results:
1,120 proteins were identified, and 82 MMD-related proteins were found with more than 1.5
fold difference compared with those in the control samples. Gene Ontology analysis showed that 29
proteins were immune-related. In particular, Haptoglobin (HP) was up-regulated in dural tissue and
plasma of MMD samples compared to the controls, and its up-regulation was found to be sex- and
MMD Suzuki grade dependent. Through Receiver Operating Characteristic (ROC) analysis, HP can
well discriminate MMD and healthy donors with the Area Under the Curve (AUC) of 0.953.
Conclusion:
We identified the biggest protein database of the dura mater. 29 out of 82 differentially
expressed proteins in MMD are involved in the immune process. Of which, HP was up-regulated in
dural tissue and plasma of MMD, with sex- and MMD Suzuki grade-dependence. HP might be a potential
biomarker of MMD.
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Affiliation(s)
- Xiaojun Zhang
- The 85th Hospital of the Chinese People's Liberation Army, Shanghai 200052, China
| | - Lin Yin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Xiaofang Jia
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yujiao Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Tiefu Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
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11
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Fu J, Luo Y, Mou M, Zhang H, Tang J, Wang Y, Zhu F. Advances in Current Diabetes Proteomics: From the Perspectives of Label- free Quantification and Biomarker Selection. Curr Drug Targets 2021; 21:34-54. [PMID: 31433754 DOI: 10.2174/1389450120666190821160207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Due to its prevalence and negative impacts on both the economy and society, the diabetes mellitus (DM) has emerged as a worldwide concern. In light of this, the label-free quantification (LFQ) proteomics and diabetic marker selection methods have been applied to elucidate the underlying mechanisms associated with insulin resistance, explore novel protein biomarkers, and discover innovative therapeutic protein targets. OBJECTIVE The purpose of this manuscript is to review and analyze the recent computational advances and development of label-free quantification and diabetic marker selection in diabetes proteomics. METHODS Web of Science database, PubMed database and Google Scholar were utilized for searching label-free quantification, computational advances, feature selection and diabetes proteomics. RESULTS In this study, we systematically review the computational advances of label-free quantification and diabetic marker selection methods which were applied to get the understanding of DM pathological mechanisms. Firstly, different popular quantification measurements and proteomic quantification software tools which have been applied to the diabetes studies are comprehensively discussed. Secondly, a number of popular manipulation methods including transformation, pretreatment (centering, scaling, and normalization), missing value imputation methods and a variety of popular feature selection techniques applied to diabetes proteomic data are overviewed with objective evaluation on their advantages and disadvantages. Finally, the guidelines for the efficient use of the computationbased LFQ technology and feature selection methods in diabetes proteomics are proposed. CONCLUSION In summary, this review provides guidelines for researchers who will engage in proteomics biomarker discovery and by properly applying these proteomic computational advances, more reliable therapeutic targets will be found in the field of diabetes mellitus.
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Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University, Chongqing 401331, China
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12
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Morello G, Salomone S, D’Agata V, Conforti FL, Cavallaro S. From Multi-Omics Approaches to Precision Medicine in Amyotrophic Lateral Sclerosis. Front Neurosci 2020; 14:577755. [PMID: 33192262 PMCID: PMC7661549 DOI: 10.3389/fnins.2020.577755] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating and fatal neurodegenerative disorder, caused by the degeneration of upper and lower motor neurons for which there is no truly effective cure. The lack of successful treatments can be well explained by the complex and heterogeneous nature of ALS, with patients displaying widely distinct clinical features and progression patterns, and distinct molecular mechanisms underlying the phenotypic heterogeneity. Thus, stratifying ALS patients into consistent and clinically relevant subgroups can be of great value for the development of new precision diagnostics and targeted therapeutics for ALS patients. In the last years, the use and integration of high-throughput "omics" approaches have dramatically changed our thinking about ALS, improving our understanding of the complex molecular architecture of ALS, distinguishing distinct patient subtypes and providing a rational foundation for the discovery of biomarkers and new individualized treatments. In this review, we discuss the most significant contributions of omics technologies in unraveling the biological heterogeneity of ALS, highlighting how these approaches are revealing diagnostic, prognostic and therapeutic targets for future personalized interventions.
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Affiliation(s)
- Giovanna Morello
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Catania, Italy
- Section of Pharmacology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Salvatore Salomone
- Section of Pharmacology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Velia D’Agata
- Human Anatomy and Histology, University of Catania, Catania, Italy
| | | | - Sebastiano Cavallaro
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Catania, Italy
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13
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Ng Kee Kwong KC, Mehta AR, Nedergaard M, Chandran S. Defining novel functions for cerebrospinal fluid in ALS pathophysiology. Acta Neuropathol Commun 2020; 8:140. [PMID: 32819425 PMCID: PMC7439665 DOI: 10.1186/s40478-020-01018-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Despite the considerable progress made towards understanding ALS pathophysiology, several key features of ALS remain unexplained, from its aetiology to its epidemiological aspects. The glymphatic system, which has recently been recognised as a major clearance pathway for the brain, has received considerable attention in several neurological conditions, particularly Alzheimer's disease. Its significance in ALS has, however, been little addressed. This perspective article therefore aims to assess the possibility of CSF contribution in ALS by considering various lines of evidence, including the abnormal composition of ALS-CSF, its toxicity and the evidence for impaired CSF dynamics in ALS patients. We also describe a potential role for CSF circulation in determining disease spread as well as the importance of CSF dynamics in ALS neurotherapeutics. We propose that a CSF model could potentially offer additional avenues to explore currently unexplained features of ALS, ultimately leading to new treatment options for people with ALS.
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Affiliation(s)
- Koy Chong Ng Kee Kwong
- UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Arpan R Mehta
- UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Siddharthan Chandran
- UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK.
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK.
- Centre for Brain Development and Repair, inStem, Bangalore, India.
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14
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Altered serum protein levels in frontotemporal dementia and amyotrophic lateral sclerosis indicate calcium and immunity dysregulation. Sci Rep 2020; 10:13741. [PMID: 32792518 PMCID: PMC7426269 DOI: 10.1038/s41598-020-70687-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are neurodegenerative diseases that are considered to be on the same disease spectrum because of overlapping genetic, pathological and clinical traits. Changes in serum proteins in FTD and ALS are poorly understood, and currently no definitive biomarkers exist for diagnosing or monitoring disease progression for either disease. Here we applied quantitative discovery proteomics to analyze protein changes in FTD (N = 72) and ALS (N = 28) patient serum compared to controls (N = 22). Twenty three proteins were significantly altered in FTD compared to controls (increased-APOL1, C3, CTSH, EIF5A, MYH2, S100A8, SUSD5, WDR1; decreased-C1S, C7, CILP2, COMP, CRTAC1, EFEMP1, FBLN1, GSN, HSPG2, IGHV1, ITIH2, PROS1, SHBG, UMOD, VASN) and 14 proteins were significantly altered in ALS compared to controls (increased-APOL1, CKM, CTSH, IGHG1, IGKC, MYH2; decreased-C7, COMP, CRTAC1, EFEMP1, FBLN1, GSN, HSPG2, SHBG). There was substantial overlap in the proteins that were altered in FTD and ALS. These results were validated using western blotting. Gene ontology tools were used to assess functional pathways potentially dysregulated in the two diseases, and calcium ion binding and innate immunity pathways were altered in both diseases. When put together, these results suggest significant overlap in pathophysiological peripheral changes in FTD and ALS. This study represents the first proteomics side-by-side comparison of serum changes in FTD and ALS, providing new insights into under-recognized perturbed pathways and an avenue for biomarker development for FTD and ALS.
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15
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Proteomic Analysis of Human Esophageal Cancer Using Tandem Mass Tag Quantifications. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5849323. [PMID: 32832552 PMCID: PMC7429764 DOI: 10.1155/2020/5849323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 01/17/2023]
Abstract
Esophageal cancer (EC) is a type of extremely aggressive gastrointestinal cancer with high incidences in China and other Asian countries. EC does not have specific symptoms and is relatively easy to metastasize, which makes it difficult in early diagnosis. Thus, novel noninvasive diagnostic method is urgently needed in clinical practice. In this study, mass spectrometry with tandem mass tags and differential protein analysis were applied for identifying esophageal cancer-related proteins. The identified proteins were annotated based on their enrichment in Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In addition, hierarchical clustering was applied based on differentially expressed proteins. As a result, a total of 5131 quantifiable proteins were identified from our liquid chromatography-tandem mass spectrometry with tandem mass tags (LC-MS/MS-TMT) method with 63 upregulated and 97 downregulated differential proteins between esophageal cancer and controlled normal samples. The differentially expressed proteins were highly enriched in GO terms associated with mitochondrial dissemble and apoptosis, and blood vessel regulation, and the upregulated differentially expressed proteins in EC samples were significantly enriched in major histocompatibility complex MHC-class I/II pathway of immune system. The functional clustering analysis revealed potential protein-protein interactions among tetraspanin, myosin, and S-100. In summary, our study provided a practical technological procedure of proteomic analysis for discovering novel biomarkers of a specific cancer type.
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16
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Ng Kee Kwong KC, Gregory JM, Pal S, Chandran S, Mehta AR. Cerebrospinal fluid cytotoxicity in amyotrophic lateral sclerosis: a systematic review of in vitro studies. Brain Commun 2020; 2:fcaa121. [PMID: 33094283 PMCID: PMC7566327 DOI: 10.1093/braincomms/fcaa121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022] Open
Abstract
Various studies have suggested that a neurotoxic cerebrospinal fluid profile could be implicated in amyotrophic lateral sclerosis. Here, we systematically review the evidence for cerebrospinal fluid cytotoxicity in amyotrophic lateral sclerosis and explore its clinical correlates. We searched the following databases with no restrictions on publication date: PubMed, Embase and Web of Science. All studies that investigated cytotoxicity in vitro following exposure to cerebrospinal fluid from amyotrophic lateral sclerosis patients were considered for inclusion. Meta-analysis could not be performed, and findings were instead narratively summarized. Twenty-eight studies were included in our analysis. Both participant characteristics and study conditions including cerebrospinal fluid concentration, exposure time and culture model varied considerably across studies. Of 22 studies assessing cell viability relative to controls, 19 studies reported a significant decrease following exposure to cerebrospinal fluid from patients with amyotrophic lateral sclerosis, while three early studies failed to observe any difference. Seven of eight studies evaluating apoptosis observed significant increases in the levels of apoptotic markers following exposure to cerebrospinal fluid from patients with amyotrophic lateral sclerosis, with the remaining study reporting a qualitative difference. Although five studies investigated the possible relationship between cerebrospinal fluid cytotoxicity and patient characteristics, such as age, gender and disease duration, none demonstrated an association with any of the factors. In conclusion, our analysis suggests that cerebrospinal fluid cytotoxicity is a feature of sporadic and possibly also of familial forms of amyotrophic lateral sclerosis. Further research is, however, required to better characterize its underlying mechanisms and to establish its possible contribution to amyotrophic lateral sclerosis pathophysiology.
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Affiliation(s)
| | - Jenna M Gregory
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.,MRC Edinburgh Brain Bank, Academic Department of Neuropathology, University of Edinburgh, Edinburgh, UK.,Edinburgh Pathology, University of Edinburgh, Edinburgh, UK
| | - Suvankar Pal
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.,Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.,Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK.,Centre for Brain Development and Repair, inStem, Bangalore, India
| | - Arpan R Mehta
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.,Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK.,Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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17
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Kadena K, Vlamos P. Amyotrophic Lateral Sclerosis: Current Status in Diagnostic Biomarkers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1195:179-187. [PMID: 32468476 DOI: 10.1007/978-3-030-32633-3_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a rare, neurodegenerative disease that affects the human motor system. ALS is a highly heterogeneous disease, depending on several causative factors. The heterogeneity of the disease is also reflected in the variation of the symptoms in ALS patients. The worldwide annual incidence of ALS is about 2.08 per 100,000 with uniform rates in Caucasian populations and lower rates in African, Asian, and Hispanic populations, while the number of individuals with ALS is expected to grow significantly between 2015 and 2040 with an estimated increase of 69% (Chio et al. 2013a; Arthur et al. 2016).
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Affiliation(s)
- Katerina Kadena
- Department of Informatics, Ionian University, Corfu, Greece.
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18
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Tang J, Fu J, Wang Y, Luo Y, Yang Q, Li B, Tu G, Hong J, Cui X, Chen Y, Yao L, Xue W, Zhu F. Simultaneous Improvement in the Precision, Accuracy, and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains. Mol Cell Proteomics 2019; 18:1683-1699. [PMID: 31097671 PMCID: PMC6682996 DOI: 10.1074/mcp.ra118.001169] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/28/2019] [Indexed: 12/13/2022] Open
Abstract
The label-free proteome quantification (LFQ) is multistep workflow collectively defined by quantification tools and subsequent data manipulation methods that has been extensively applied in current biomedical, agricultural, and environmental studies. Despite recent advances, in-depth and high-quality quantification remains extremely challenging and requires the optimization of LFQs by comparatively evaluating their performance. However, the evaluation results using different criteria (precision, accuracy, and robustness) vary greatly, and the huge number of potential LFQs becomes one of the bottlenecks in comprehensively optimizing proteome quantification. In this study, a novel strategy, enabling the discovery of the LFQs of simultaneously enhanced performance from thousands of workflows (integrating 18 quantification tools with 3,128 manipulation chains), was therefore proposed. First, the feasibility of achieving simultaneous improvement in the precision, accuracy, and robustness of LFQ was systematically assessed by collectively optimizing its multistep manipulation chains. Second, based on a variety of benchmark datasets acquired by various quantification measurements of different modes of acquisition, this novel strategy successfully identified a number of manipulation chains that simultaneously improved the performance across multiple criteria. Finally, to further enhance proteome quantification and discover the LFQs of optimal performance, an online tool (https://idrblab.org/anpela/) enabling collective performance assessment (from multiple perspectives) of the entire LFQ workflow was developed. This study confirmed the feasibility of achieving simultaneous improvement in precision, accuracy, and robustness. The novel strategy proposed and validated in this study together with the online tool might provide useful guidance for the research field requiring the mass-spectrometry-based LFQ technique.
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Affiliation(s)
- Jing Tang
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China; ¶Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, China
| | - Jianbo Fu
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunxia Wang
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qingxia Yang
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Bo Li
- §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Gao Tu
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jiajun Hong
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xuejiao Cui
- §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yuzong Chen
- ‖Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Lixia Yao
- **Department of Health Sciences Research, Mayo Clinic, Rochester MN 55905, United States
| | - Weiwei Xue
- §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China.
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19
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Hedl TJ, San Gil R, Cheng F, Rayner SL, Davidson JM, De Luca A, Villalva MD, Ecroyd H, Walker AK, Lee A. Proteomics Approaches for Biomarker and Drug Target Discovery in ALS and FTD. Front Neurosci 2019; 13:548. [PMID: 31244593 PMCID: PMC6579929 DOI: 10.3389/fnins.2019.00548] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are increasing in prevalence but lack targeted therapeutics. Although the pathological mechanisms behind these diseases remain unclear, both ALS and FTD are characterized pathologically by aberrant protein aggregation and inclusion formation within neurons, which correlates with neurodegeneration. Notably, aggregation of several key proteins, including TAR DNA binding protein of 43 kDa (TDP-43), superoxide dismutase 1 (SOD1), and tau, have been implicated in these diseases. Proteomics methods are being increasingly applied to better understand disease-related mechanisms and to identify biomarkers of disease, using model systems as well as human samples. Proteomics-based approaches offer unbiased, high-throughput, and quantitative results with numerous applications for investigating proteins of interest. Here, we review recent advances in the understanding of ALS and FTD pathophysiology obtained using proteomics approaches, and we assess technical and experimental limitations. We compare findings from various mass spectrometry (MS) approaches including quantitative proteomics methods such as stable isotope labeling by amino acids in cell culture (SILAC) and tandem mass tagging (TMT) to approaches such as label-free quantitation (LFQ) and sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) in studies of ALS and FTD. Similarly, we describe disease-related protein-protein interaction (PPI) studies using approaches including immunoprecipitation mass spectrometry (IP-MS) and proximity-dependent biotin identification (BioID) and discuss future application of new techniques including proximity-dependent ascorbic acid peroxidase labeling (APEX), and biotinylation by antibody recognition (BAR). Furthermore, we explore the use of MS to detect post-translational modifications (PTMs), such as ubiquitination and phosphorylation, of disease-relevant proteins in ALS and FTD. We also discuss upstream technologies that enable enrichment of proteins of interest, highlighting the contributions of new techniques to isolate disease-relevant protein inclusions including flow cytometric analysis of inclusions and trafficking (FloIT). These recently developed approaches, as well as related advances yet to be applied to studies of these neurodegenerative diseases, offer numerous opportunities for discovery of potential therapeutic targets and biomarkers for ALS and FTD.
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Affiliation(s)
- Thomas J Hedl
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Rebecca San Gil
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Flora Cheng
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Jennilee M Davidson
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Alana De Luca
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Maria D Villalva
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Heath Ecroyd
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Adam K Walker
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia.,Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
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20
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Moreno-Martinez L, Calvo AC, Muñoz MJ, Osta R. Are Circulating Cytokines Reliable Biomarkers for Amyotrophic Lateral Sclerosis? Int J Mol Sci 2019; 20:ijms20112759. [PMID: 31195629 PMCID: PMC6600567 DOI: 10.3390/ijms20112759] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that has no effective treatment. The lack of any specific biomarker that can help in the diagnosis or prognosis of ALS has made the identification of biomarkers an urgent challenge. Multiple panels have shown alterations in levels of numerous cytokines in ALS, supporting the contribution of neuroinflammation to the progressive motor neuron loss. However, none of them is fully sensitive and specific enough to become a universal biomarker for ALS. This review gathers the numerous circulating cytokines that have been found dysregulated in both ALS animal models and patients. Particularly, it highlights the opposing results found in the literature to date, and points out another potential application of inflammatory cytokines as therapeutic targets.
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Affiliation(s)
- Laura Moreno-Martinez
- Laboratory of Genetics and Biochemistry (LAGENBIO), Faculty of Veterinary-IIS Aragón, IA2-CITA, CIBERNED, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain.
| | - Ana Cristina Calvo
- Laboratory of Genetics and Biochemistry (LAGENBIO), Faculty of Veterinary-IIS Aragón, IA2-CITA, CIBERNED, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain.
| | - María Jesús Muñoz
- Laboratory of Genetics and Biochemistry (LAGENBIO), Faculty of Veterinary-IIS Aragón, IA2-CITA, CIBERNED, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain.
| | - Rosario Osta
- Laboratory of Genetics and Biochemistry (LAGENBIO), Faculty of Veterinary-IIS Aragón, IA2-CITA, CIBERNED, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain.
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21
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Swindell WR, Kruse CPS, List EO, Berryman DE, Kopchick JJ. ALS blood expression profiling identifies new biomarkers, patient subgroups, and evidence for neutrophilia and hypoxia. J Transl Med 2019; 17:170. [PMID: 31118040 PMCID: PMC6530130 DOI: 10.1186/s12967-019-1909-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/07/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a debilitating disease with few treatment options. Progress towards new therapies requires validated disease biomarkers, but there is no consensus on which fluid-based measures are most informative. METHODS This study analyzed microarray data derived from blood samples of patients with ALS (n = 396), ALS mimic diseases (n = 75), and healthy controls (n = 645). Goals were to provide in-depth analysis of differentially expressed genes (DEGs), characterize patient-to-patient heterogeneity, and identify candidate biomarkers. RESULTS We identified 752 ALS-increased and 764 ALS-decreased DEGs (FDR < 0.10 with > 10% expression change). Gene expression shifts in ALS blood broadly resembled acute high altitude stress responses. ALS-increased DEGs had high exosome expression, were neutrophil-specific, associated with translation, and overlapped significantly with genes near ALS susceptibility loci (e.g., IFRD1, TBK1, CREB5). ALS-decreased DEGs, in contrast, had low exosome expression, were erythroid lineage-specific, and associated with anemia and blood disorders. Genes encoding neurofilament proteins (NEFH, NEFL) had poor diagnostic accuracy (50-53%). However, support vector machines distinguished ALS patients from ALS mimics and controls with 87% accuracy (sensitivity: 86%, specificity: 87%). Expression profiles were heterogeneous among patients and we identified two subgroups: (i) patients with higher expression of IL6R and myeloid lineage-specific genes and (ii) patients with higher expression of IL23A and lymphoid-specific genes. The gene encoding copper chaperone for superoxide dismutase (CCS) was most strongly associated with survival (HR = 0.77; P = 1.84e-05) and other survival-associated genes were linked to mitochondrial respiration. We identify a 61 gene signature that significantly improves survival prediction when added to Cox proportional hazard models with baseline clinical data (i.e., age at onset, site of onset and sex). Predicted median survival differed 2-fold between patients with favorable and risk-associated gene expression signatures. CONCLUSIONS Peripheral blood analysis informs our understanding of ALS disease mechanisms and genetic association signals. Our findings are consistent with low-grade neutrophilia and hypoxia as ALS phenotypes, with heterogeneity among patients partly driven by differences in myeloid and lymphoid cell abundance. Biomarkers identified in this study require further validation but may provide new tools for research and clinical practice.
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Affiliation(s)
- William R. Swindell
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
- Department of Internal Medicine, The Jewish Hospital, Cincinnati, OH 45236 USA
| | - Colin P. S. Kruse
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701 USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701 USA
| | - Edward O. List
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701 USA
- The Diabetes Institute, Ohio University, Athens, OH 45701 USA
| | - Darlene E. Berryman
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701 USA
- The Diabetes Institute, Ohio University, Athens, OH 45701 USA
| | - John J. Kopchick
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701 USA
- The Diabetes Institute, Ohio University, Athens, OH 45701 USA
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22
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Verber NS, Shepheard SR, Sassani M, McDonough HE, Moore SA, Alix JJP, Wilkinson ID, Jenkins TM, Shaw PJ. Biomarkers in Motor Neuron Disease: A State of the Art Review. Front Neurol 2019; 10:291. [PMID: 31001186 PMCID: PMC6456669 DOI: 10.3389/fneur.2019.00291] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/06/2019] [Indexed: 12/17/2022] Open
Abstract
Motor neuron disease can be viewed as an umbrella term describing a heterogeneous group of conditions, all of which are relentlessly progressive and ultimately fatal. The average life expectancy is 2 years, but with a broad range of months to decades. Biomarker research deepens disease understanding through exploration of pathophysiological mechanisms which, in turn, highlights targets for novel therapies. It also allows differentiation of the disease population into sub-groups, which serves two general purposes: (a) provides clinicians with information to better guide their patients in terms of disease progression, and (b) guides clinical trial design so that an intervention may be shown to be effective if population variation is controlled for. Biomarkers also have the potential to provide monitoring during clinical trials to ensure target engagement. This review highlights biomarkers that have emerged from the fields of systemic measurements including biochemistry (blood, cerebrospinal fluid, and urine analysis); imaging and electrophysiology, and gives examples of how a combinatorial approach may yield the best results. We emphasize the importance of systematic sample collection and analysis, and the need to correlate biomarker findings with detailed phenotype and genotype data.
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Affiliation(s)
- Nick S Verber
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Stephanie R Shepheard
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Matilde Sassani
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Harry E McDonough
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Sophie A Moore
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - James J P Alix
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Iain D Wilkinson
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Tom M Jenkins
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Pamela J Shaw
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
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23
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Mitropoulos K, Katsila T, Patrinos GP, Pampalakis G. Multi-Omics for Biomarker Discovery and Target Validation in Biofluids for Amyotrophic Lateral Sclerosis Diagnosis. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 22:52-64. [PMID: 29356625 DOI: 10.1089/omi.2017.0183] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a rare but usually fatal neurodegenerative disease characterized by motor neuron degeneration in the brain and the spinal cord. Two forms are recognized, the familial that accounts for 5-10% and the sporadic that accounts for the rest. New studies suggest that ALS is a highly heterogeneous disease, and this diversity is a major reason for the lack of successful therapeutic treatments. Indeed, only two drugs (riluzole and edaravone) have been approved that provide a limited improvement in the quality of life. Presently, the diagnosis of ALS is based on clinical examination and lag period from the onset of symptoms to the final diagnosis is ∼12 months. Therefore, the discovery of robust molecular biomarkers that can assist in the diagnosis is of major importance. DNA sequencing to identify pathogenic gene variants can be applied in the cases of familial ALS. However, it is not a routinely used diagnostic procedure and most importantly, it cannot be applied in the diagnosis of sporadic ALS. In this expert review, the current approaches in identification of new ALS biomarkers are discussed. The advent of various multi-omics biotechnology platforms, including miRNomics, proteomics, metabolomics, metallomics, volatolomics, and viromics, has assisted in the identification of new biomarkers. The biofluids are the most preferable material for the analysis of potential biomarkers (such as proteins and cell-free miRNAs), since they are easily obtained. In the near future, the biofluid-based biomarkers will be indispensable to classify different ALS subtypes and understand the molecular heterogeneity of the disease.
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Affiliation(s)
- Konstantinos Mitropoulos
- 1 Department of Histology and Embryology, University of Athens School of Medicine , Athens, Greece
| | - Theodora Katsila
- 2 Department of Pharmacy, University of Patras School of Health Sciences , Patras, Greece
| | - George P Patrinos
- 2 Department of Pharmacy, University of Patras School of Health Sciences , Patras, Greece .,3 Department of Pharmacy, College of Medicine and Health Sciences, United Arab Emirates University , Al Ain, UAE
| | - Georgios Pampalakis
- 2 Department of Pharmacy, University of Patras School of Health Sciences , Patras, Greece
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24
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Campanari ML, Bourefis AR, Kabashi E. Diagnostic Challenge and Neuromuscular Junction Contribution to ALS Pathogenesis. Front Neurol 2019; 10:68. [PMID: 30787905 PMCID: PMC6372519 DOI: 10.3389/fneur.2019.00068] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/17/2019] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) represents the major adult-onset motor neuron disease. Both human and animal studies reveal the critical implication of muscle and neuromuscular junctions (NMJs) in the initial phase of this disease. Despite the common efforts, ALS diagnosis remains particularly challenging since many other disorders can overlap yielding similar clinical phenotypic features. A combination of further research on the NMJ parameters that are specific for this disease and laboratory tests are crucial for the early determination of specific changes in the muscle, as well as in motor neuron and the prediction of ALS progression. Also, it could provide a powerful tool in the discrimination of particular ALS and ALS-mimic cases and increase the efficacy of therapeutic treatments.
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Affiliation(s)
- Maria-Letizia Campanari
- Sorbonne Université, Université Pierre et Marie Curie, Université de Paris 06, Unité Mixte 75, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1127, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière, Paris, France.,Imagine Institute, INSERM Unité 1163, Paris Descartes Université, Paris, France
| | - Annis-Rayan Bourefis
- Sorbonne Université, Université Pierre et Marie Curie, Université de Paris 06, Unité Mixte 75, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1127, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière, Paris, France.,Imagine Institute, INSERM Unité 1163, Paris Descartes Université, Paris, France
| | - Edor Kabashi
- Sorbonne Université, Université Pierre et Marie Curie, Université de Paris 06, Unité Mixte 75, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1127, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière, Paris, France.,Imagine Institute, INSERM Unité 1163, Paris Descartes Université, Paris, France
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25
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Murphy S, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Proteomic serum biomarkers for neuromuscular diseases. Expert Rev Proteomics 2018; 15:277-291. [DOI: 10.1080/14789450.2018.1429923] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
| | - Margit Zweyer
- Department of Physiology II, University of Bonn, Bonn, Germany
| | | | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
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