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J Proteome Res. 2018 Dec 7;17(12):4072-4084. doi: 10.1021/acs.jproteome.8b00401. Epub 2018 Sep 28.

Biology/Disease-Driven Initiative on Protein-Aggregation Diseases of the Human Proteome Project: Goals and Progress to Date.

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Institute of Molecular Systems Biology, Department of Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland.
Department of Rheumatology & Clinical Immunology , University of Groningen, University Medical Center Groningen , Hanzeplein 1 , 9713 GZ Groningen , The Netherlands.
Clinical Protein Science & Imaging, Department of Biomedical Engineering , Lund University, BMC D13 , 221 84 Lund , Sweden.
Laboratory of Veterinary Pathology , Azabu University , 1-17-71 Fuchinobe , Chuo-ku, Sagamihara , Kanagawa 252-5201 , Japan.
Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry , The Sahlgrenska Academy at University of Gothenburg , S-431 80 Mölndal , Sweden.
Clinical Neurochemistry Laboratory , Sahlgrenska University Hospital , Mölndal S-431 80 , Sweden.
Department of Medical Biochemistry and Biophysics , Karolinska Institute , 17177 Stockholm , Sweden.
Institute of Molecular Life Sciences, University of Zürich , Winterthurerstrasse 190 , Zürich , Switzerland.


The Biology/Disease-driven (B/D) working groups of the Human Proteome Project are alliances of research groups aimed at developing or improving proteomic tools to support specific biological or disease-related research areas. Here, we describe the activities and progress to date of the B/D working group focused on protein aggregation diseases (PADs). PADs are characterized by the intra- or extracellular accumulation of aggregated proteins and include devastating diseases such as Parkinson's and Alzheimer's disease and systemic amyloidosis. The PAD B/D working group aims for the development of proteomic assays for the quantification of aggregation-prone proteins involved in PADs to support basic and clinical research on PADs. Because the proteins in PADs undergo aberrant conformational changes, a goal is to quantitatively resolve altered protein structures and aggregation states in complex biological specimens. We have developed protein-extraction protocols and a set of mass spectrometric (MS) methods that enable the detection and quantification of proteins involved in the systemic and localized amyloidosis and the probing of aberrant protein conformational transitions in cell and tissue extracts. In several studies, we have demonstrated the potential of MS-based proteomics approaches for specific and sensitive clinical diagnoses and for the subtyping of PADs. The developed methods have been detailed in both protocol papers and manuscripts describing applications to facilitate implementation by nonspecialized laboratories, and assay coordinates are shared through public repositories and databases. Clinicians actively involved in the PAD working group support the transfer to clinical practice of the developed methods, such as assays to quantify specific disease-related proteins and their fragments in biofluids and multiplexed MS-based methods for the diagnosis and typing of systemic amyloidosis. We believe that the increasing availability of tools to precisely measure proteins involved in PADs will positively impact research on the molecular bases of these diseases and support early disease diagnosis and a more-confident subtyping.


Alzheimer’s disease; Biology/Disease-driven HPP; Human Proteome Project; Parkinson’s disease; amyotrophic lateral sclerosis; frontotemporal dementia; protein-aggregation diseases; systemic amyloidosis

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