Proteomics approaches for biomarker and drug target discovery in ALS and FTD

Thomas J. Hedl, Rebecca San Gil, Flora Cheng, Stephanie L. Rayner, Jennilee M. Davidson, Alana De Luca, Maria D. Villalva, Heath Ecroyd, Adam K. Walker, Albert Lee

Research output: Contribution to journalReview articleResearchpeer-review

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.

LanguageEnglish
Article number548
Pages1-25
Number of pages25
JournalFrontiers in Neuroscience
Volume13
DOIs
Publication statusPublished - 11 Jun 2019

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Drug Discovery
Proteomics
Biomarkers
Proteins
Mass Spectrometry
Neurodegenerative Diseases
Isotope Labeling
Biotinylation
Frontotemporal Dementia With Motor Neuron Disease
Ubiquitination
DNA-Binding Proteins
Post Translational Protein Processing
Biotin
Immunoprecipitation
Peroxidase
Ascorbic Acid
Cell Culture Techniques
Phosphorylation
Ions
Technology

Bibliographical note

Copyright the Author(s) 2019. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

  • amyotrophic lateral sclerosis
  • frontotemporal dementia
  • proteomics
  • mass spectrometry
  • protein aggregation

Cite this

Hedl, Thomas J. ; San Gil, Rebecca ; Cheng, Flora ; Rayner, Stephanie L. ; Davidson, Jennilee M. ; De Luca, Alana ; Villalva, Maria D. ; Ecroyd, Heath ; Walker, Adam K. ; Lee, Albert. / Proteomics approaches for biomarker and drug target discovery in ALS and FTD. In: Frontiers in Neuroscience. 2019 ; Vol. 13. pp. 1-25.
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Proteomics approaches for biomarker and drug target discovery in ALS and FTD. / Hedl, Thomas J.; San Gil, Rebecca; Cheng, Flora; Rayner, Stephanie L.; Davidson, Jennilee M.; De Luca, Alana; Villalva, Maria D.; Ecroyd, Heath; Walker, Adam K.; Lee, Albert.

In: Frontiers in Neuroscience, Vol. 13, 548, 11.06.2019, p. 1-25.

Research output: Contribution to journalReview articleResearchpeer-review

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T1 - Proteomics approaches for biomarker and drug target discovery in ALS and FTD

AU - Hedl,Thomas J.

AU - San Gil,Rebecca

AU - Cheng,Flora

AU - Rayner,Stephanie L.

AU - Davidson,Jennilee M.

AU - De Luca,Alana

AU - Villalva,Maria D.

AU - Ecroyd,Heath

AU - Walker,Adam K.

AU - Lee,Albert

N1 - Copyright the Author(s) 2019. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

PY - 2019/6/11

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N2 - 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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KW - amyotrophic lateral sclerosis

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