Molecular and Clinical Aspects of Protein Aggregation Assays in Neurodegenerative Diseases

Different Chronic Stress Paradigms Converge on Endogenous TDP43 Cleavage and Aggregation

The TAR-DNA binding protein (TDP43) is a nuclear protein whose cytoplasmic inclusions are hallmarks of Amyotrophic Lateral Sclerosis (ALS). Acute stress in cells causes TDP43 mobilization to the cytoplasm and its aggregation through different routes. Although acute stress elicits a strong phenotype, is far from recapitulating the years-long aggregation process. We applied different chronic stress protocols and described TDP43 aggregation in a human neuroblastoma cell line by combining solubility assays, thioflavin-based microscopy and flow cytometry. This approach allowed us to detect, for the first time to our knowledge in vitro, the formation of 25 kDa C-terminal fragment of TDP43, a pathogenic hallmark of ALS. Our results indicate that chronic stress, compared to the more common acute stress paradigm, better recapitulates the cell biology of TDP43 proteinopathies. Moreover, we optimized a protocol for the detection of bona fide prions in living cells, suggesting that TDP43 may form amyloids as a stress response.

Development of an in vitro aggregation assay for long synthetic polypeptide, amyloidogenic gelsolin fragment AGelD187N 173-242

Aggregation of the gelsolin protein fragment is the hallmark of the hereditary systemic disease gelsolin amyloidosis. As with other protein misfolding diseases, there is an urgent need for efficient disease-modifying treatment for gelsolin amyloidosis. The formation of amyloids can be reproduced by incubating the disease-causing amyloidogenic 8 kDa polypeptide, 70-residue gelsolin protein fragment, AGelD187N 173-242, in vitro and monitoring the process by thioflavin T dye. However, for screening of potential aggregation inhibitors, the required protein amounts are large and the biotechnological production of amyloidogenic proteins has many challenges. Conversely, use of shorter synthetic regions of AGelD187N 173-242 does not mimic the in vivo aggregation kinetics of full-length fragment as they have different aggregation propensity. In this study, we present an in vitro aggregation assay for full-length AGelD187N 173-242 that has been produced by solid-phase chemical synthesis and after that monomerized carefully. Chemical synthesis allows us to produce high quantities of full-length fragment efficiently and at low cost. We demonstrate that the generated aggregates are fibrillar in nature and how the purity, terminal modification, initial aggregates and seeding affect the aggregation kinetics of a synthetic gelsolin fragment. We also present sufficient quality criteria for the initial monomerized synthetic polypeptide.

A Comprehensive Analysis of the Intrinsic Visible Fluorescence Emitted by Peptide/Protein Amyloid-like Assemblies

Amyloid aggregation is a widespread process that involves proteins and peptides with different molecular complexity and amino acid composition. The structural motif (cross-β) underlying this supramolecular organization generates aggregates endowed with special mechanical and spectroscopic properties with huge implications in biomedical and technological fields, including emerging precision medicine. The puzzling ability of these assemblies to emit intrinsic and label-free fluorescence in regions of the electromagnetic spectrum, such as visible and even infrared, usually considered to be forbidden in the polypeptide chain, has attracted interest for its many implications in both basic and applied science. Despite the interest in this phenomenon, the physical basis of its origin is still poorly understood. To gain a global view of the available information on this phenomenon, we here provide an exhaustive survey of the current literature in which original data on this fluorescence have been reported. The emitting systems have been classified in terms of their molecular complexity, amino acid composition, and physical state. Information about the wavelength of the radiation used for the excitation as well as the emission range/peak has also been retrieved. The data collected here provide a picture of the complexity of this multifaceted phenomenon that could be helpful for future studies aimed at defining its structural and electronic basis and/or stimulating new applications.

Molecular weight and molecular weight distribution of sericin protein extracted from cocoon waste of <i>Bombyx mori</i>

Silk sericin comprises a globular water-soluble protein that surrounds silk fibres, sticking them together and providing cocoon adhesion. Sericin was isolated from the extract solution in two ways: the first sample was obtained by concentrating the filtered extract at low pressure (SLP); the second sample was obtained by ultrafiltration (SUF) using a membrane. In this work, the size exclusion-high-performance liquid chromatography involving viscometry and refractive index detectors was used to determine the molecular weight and conformation of sericin polypeptides obtained from cocoons of the Bombyx mori silkworm. The aggregation processes of silk sericin protein under various isolation conditions from the solution were considered. It was shown that sericin macromolecules are present as a monodisperse polypeptide at low concentrations, which aggregates at concentrations greater than 1–2 mg/ml. The obtained data indicate that, along with the parameters of the extraction process, the conditions for its isolation from the solution, including temperature, pressure and degree of concentration, affect the molecular weight and aggregative behaviour of the protein. The results confirm and complement previously obtained data on the influence of various factors on the association of protein macromolecules in solution. The resulting sericin fractions can find many applications, including materials for tissue engineering, coatings for surface modification, cell culture media, cosmetics, as well as food additives and medical biomaterials.

Impact of denaturing agents on surface properties of myoglobin solutions

The addition of denaturants strongly influences the surface properties of aqueous myoglobin solutions. The effect differs from the results for mixed solutions of the denaturants and other globular proteins, for example, bovine serum albumin (BSA), lysozyme and β-lactoglobulin (BLG), although the surface properties of the solutions of the pure proteins are similar. The kinetic dependencies of the dynamic surface elasticity of myoglobin solutions with guanidine hydrochloride (GuHCl) reveal at least two adsorption steps at denaturant concentrations higher than 1 M: a very fast increase of the dynamic surface elasticity to approximately 30 mN/m at the beginning of adsorption, and a slower growth to abnormally high values of 250-300 mN/m. At the same time, the surface elasticity of BSA/GuHCl, BLG/GuHCl and lysozyme/GuHCl solutions is a non-monotonic function of the surface age, and does not exceed 50 mN/m close to equilibrium. The high surface elasticity of myoglobin/GuHCl solutions may be associated with protein aggregation in the surface layer. The formation of aggregates is confirmed by ellipsometry and Brewster angle microscopy. The addition of ionic surfactants to protein solutions leads to the formation of myoglobin/surfactant complexes, and the kinetic dependencies of the dynamic surface elasticity display local maxima indicating multistep adsorption kinetics, unlike the corresponding results for solutions of other globular proteins mixed with ionic surfactants. Ellipsometry and infrared reflection-absorption spectroscopy allow tracing the adsorption of the complexes and their displacement from the interface at high surfactant concentrations.

Adsorption layer formation in dispersions of protein aggregates

The review discusses recent results on the adsorption of amyloid fibrils and protein microgels at liquid/fluid interfaces. The application of the shear and dilational surface rheology, atomic force microscopy and passive particle probe tracking allowed for elucidating characteristic features of the protein aggregate adsorption while some proposed hypothesis still must be examined by special methods for structural characterization. Although the distinctions of the shear surface properties of dispersions of protein aggregates from the properties of native protein solutions are higher than the corresponding distinctions of the dilational surface properties, the latter ones give a possibility to obtain new information on the formation of fibril aggregates at the water/air interface. Only the adsorption of BLG microgels and fibrils was studied in some details. The kinetic dependencies of the dynamic surface tension and dilational surface elasticity for aqueous dispersions of protein globules, protein microgels and purified fibrils are similar if the system does not contain flexible macromolecules or flexible protein fragments. In the opposite case the kinetic dependencies of the dynamic surface elasticity can be non-monotonic. The solution pH influences strongly the dynamic surface properties of the dispersions of protein aggregates indicating that the adsorption kinetics is controlled by an electrostatic adsorption barrier if the pH deviates from the isoelectric point. A special section of the review considers the possibility to apply kinetic models of nanoparticle adsorption to the adsorption of protein aggregates.

Effect of the micro-environment on α-synuclein conversion and implication in seeded conversion assays

Background

α-Synuclein is a small soluble protein, whose physiological function in the healthy brain is poorly understood. Intracellular inclusions of α-synuclein, referred to as Lewy bodies (LBs), are pathological hallmarks of α-synucleinopathies, such as Parkinson’s disease (PD) or dementia with Lewy bodies (DLB).

Main body

Understanding of the molecular basis as well as the factors or conditions promoting α-synuclein misfolding and aggregation is an important step towards the comprehension of pathological mechanism of α-synucleinopathies and for the development of efficient therapeutic strategies. Based on the conversion and aggregation mechanism of α-synuclein, novel diagnostic tests, such as protein misfolding seeded conversion assays, e.g. the real-time quaking-induced conversion (RT-QuIC), had been developed. In diagnostics, α-synuclein RT-QuIC exhibits a specificity between 82 and 100% while the sensitivity varies between 70 and 100% among different laboratories. In addition, the α-synuclein RT-QuIC can be used to study the α-synuclein-seeding-characteristics of different α-synucleinopathies and to differentiate between DLB and PD.

Conclusion

The variable diagnostic accuracy of current α-synuclein RT-QuIC occurs due to different protocols, cohorts and material etc.. An impact of micro-environmental factors on the α-synuclein aggregation and conversion process and the occurrence and detection of differential misfolded α-synuclein types or strains might underpin the clinical heterogeneity of α-synucleinopathies.

The cellular prion protein and its derived fragments in human prion diseases and their role as potential biomarkers

Introduction: Human prion diseases are a heterogeneous group of incurable and debilitating conditions characterized by a progressive degeneration of the central nervous system. The conformational changes of the cellular prion protein and its formation into an abnormal isoform, spongiform degeneration, neuronal loss, and neuroinflammation are central to prion disease pathogenesis. It has been postulated that truncated variants of aggregation-prone proteins are implicated in neurodegenerative mechanisms. An increasing body of evidence indicates that proteolytic fragments and truncated variants of the prion protein are formed and accumulated in the brain of prion disease patients. These prion protein variants provide a high degree of relevance to disease pathology and diagnosis. Areas covered: In the present review, we summarize the current knowledge on the occurrence of truncated prion protein species and their potential roles in pathophysiological states during prion diseases progression. In addition, we discuss their usability as a diagnostic biomarker in prion diseases. Expert opinion: Either as a primary factor in the formation of prion diseases or as a consequence from neuropathological affection, abnormal prion protein variants and fragments may provide independent information about mechanisms of prion conversion, pathological states, or disease progression.

Seeding variability of different alpha synuclein strains in synucleinopathies

OBJECTIVES

Currently, the exact reasons why different α-synucleinopathies exhibit variable pathologies and phenotypes are still unknown. A potential explanation may be the existence of distinctive α-synuclein conformers or strains. Here, we intend to analyze the seeding activity of dementia with Lewy bodies (DLB) and Parkinson's disease (PD) brain-derived α-synuclein seeds by real-time quaking-induced conversion (RT-QuIC) and to investigate the structure and morphology of the α-synuclein aggregates generated by RT-QuIC.

METHODS

A misfolded α-synuclein-enriched brain fraction from frontal cortex and substantia nigra pars compacta tissue, isolated by several filtration and centrifugation steps, was subjected to α-synuclein/RT-QuIC analysis. Our study included neuropathologically well-characterized cases with DLB, PD, and controls (Ctrl). Biochemical and morphological analyses of RT-QuIC products were conducted by western blot, dot blot analysis, Raman spectroscopy, atomic force microscopy, and transmission electron microscopy.

RESULTS

Independently from the brain region, we observed different seeding kinetics of α-synuclein in the RT-QuIC in patients with DLB compared to PD and Ctrl. Biochemical characterization of the RT-QuIC product indicated the generation of a proteinase K-resistant and fibrillary α-synuclein species in DLB-seeded reactions, whereas PD and control seeds failed in the conversion of wild-type α-synuclein substrate.

INTERPRETATION

Structural variances of α-synuclein seeding kinetics and products in DLB and PD indicated, for the first time, the existence of different α-synuclein strains in these groups. Therefore, our study contributes to a better understanding of the clinical heterogeneity among α-synucleinopathies, offers an opportunity for a specific diagnosis, and opens new avenues for the future development of strain-specific therapies. Ann Neurol 2019;85:691-703.

Nucleotides regulate the common molecular mechanisms that underlie neurodegenerative diseases; Therapeutic implications

Neurodegenerative diseases (ND) are a heterogeneous group of neurological disorders characterized by a progressive loss of neuronal function which results in neuronal death. Although a specific toxic factor has been identified for each ND, all of them share common pathological molecular mechanisms favouring the disease development. In the final stages of ND, patients become unable to take care of themselves and decline to a total functional incapacitation that leads to their death. Some of the main factors which contribute to the disease progression include proteasomal dysfunction, neuroinflammation, synaptic alterations, protein aggregation, and oxidative stress. Over recent years, evidence has been accumulated to suggest that purinergic signaling plays a key role in the aforementioned molecular pathways. In this review, we revise the implications of the purinergic signaling in the common molecular mechanism underlying the ND. In particular, we focus on the role of the purinergic receptors P2X7, P2Y₂ and the ectoenzyme tissue-nonspecific alkaline phosphatase (TNAP).

Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification

Amyloids are unbranched protein fibrils with a characteristic spatial structure. Although the amyloids were first described as protein deposits that are associated with the diseases, today it is becoming clear that these protein fibrils play multiple biological roles that are essential for different organisms, from archaea and bacteria to humans. The appearance of amyloid, first of all, causes changes in the intracellular quantity of the corresponding soluble protein(s), and at the same time the aggregate can include other proteins due to different molecular mechanisms. The co-aggregation may have different consequences even though usually this process leads to the depletion of a functional protein that may be associated with different diseases. The protein co-aggregation that is related to functional amyloids may mediate important biological processes and change of protein functions. In this review, we survey the known examples of the amyloid-related co-aggregation of proteins, discuss their pathogenic and functional roles, and analyze methods of their studies from bacteria and yeast to mammals. Such analysis allow for us to propose the following co-aggregation classes: (i) titration: deposition of soluble proteins on the amyloids formed by their functional partners, with such interactions mediated by a specific binding site; (ii) sequestration: interaction of amyloids with certain proteins lacking a specific binding site; (iii) axial co-aggregation of different proteins within the same amyloid fibril; and, (iv) lateral co-aggregation of amyloid fibrils, each formed by different proteins.

Alterations in neuronal metabolism contribute to the pathogenesis of prion disease

Neurodegenerative conditions are characterised by a progressive loss of neurons, which is believed to be initiated by misfolded protein aggregations. During this time period, many physiological and metabolomic alterations and changes in gene expression contribute to the decline in neuronal function. However, these pathological effects have not been fully characterised. In this study, we utilised a metabolomic approach to investigate the metabolic changes occurring in the hippocampus and cortex of mice infected with misfolded prion protein. In order to identify these changes, the samples were analysed by ultrahigh-performance liquid chromatography-tandem mass spectroscopy. The present dataset comprises a total of 498 compounds of known identity, named biochemicals, which have undergone principal component analysis and supervised machine learning. The results generated are consistent with the prion-inoculated mice having significantly altered metabolic profiles. In particular, we highlight the alterations associated with the metabolism of glucose, neuropeptides, fatty acids, L-arginine/nitric oxide and prostaglandins, all of which undergo significant changes during the disease. These data provide possibilities for future studies targeting and investigating specific pathways to better understand the processes involved in neuronal dysfunction in neurodegenerative diseases.