Novel proteinaceous infectious particles cause scrapie

Soluble N-Terminal Domain of the Prion Protein Interferes with Fibrillization of α-Synuclein to Form Off-Pathway Assemblies that Lack Cellular Seeding Activity

Disease progression in synucleinopathies is associated with the formation of seeding-competent α-synuclein (αSyn) aggregates. After spreading and cellular uptake, the αSyn seeds propagate in a prion-like mechanism by inducing the conversion of natively folded αSyn into pathogenic aggregates. Here we show that the soluble intrinsically disordered N-terminal domain of the cellular prion protein (N1-PrP) modulates fibrillization of αSyn to form off-pathway aggregates that lack seeding activity in cells. N1-PrP does not interact with soluble αSyn. However, during the aggregation of αSyn in vitro, N1-PrP is recruited and incorporated. As a result, amorphous coaggregates are formed instead of seeding-competent αSyn fibrils. Similarly, in the cytosol of neuronal cells N-PrP specifically interacts with αSyn during the prion-like propagation of pathogenic αSyn seeds. These findings identify a unique neuroprotective activity of the soluble N-terminal domain of the prion protein by promoting off-pathway reactions in amyloid seed formation.

Downregulation of STAT3 transcription factor reverses synaptotoxic phenotype of reactive astrocytes associated with prion diseases

In neurodegenerative diseases, including prion diseases, astrocytes adopt reactive phenotypes that persist throughout disease progression. While astrocyte reactivity may initially serve as a protective response to prion infection, it transitions into a neurotoxic phenotype that disrupts homeostatic functions and exacerbates disease pathology. The transcription factor Stat3 has been recognized as a master regulator of astrocyte reactivity in neurodegenerative diseases, yet its role in prion disease-associated astrocyte reactive phenotypes remains unexplored. The current study addresses this gap by investigating the effects of Stat3 deletion in reactive astrocytes isolated from prion-infected mice. We demonstrate that Stat3 deletion mitigates the reactive astrocyte phenotype and alleviates their synaptotoxic effects. Stat3-dependent activation of astrocytes was reproduced by co-culturing naïve astrocytes with reactive microglia isolated from prion-infected animals or exposing them to microglia-conditioned media. A cytokine array profiling of 40 molecules revealed partially overlapping inflammatory signatures in reactive microglia and astrocytes, with IL-6 prominently upregulated in both cell types. Notably, IL-6 treatment elevated phosphorylated Stat3 levels in naïve astrocytes and triggered astrocyte reactivity. These findings indicate that the synaptotoxic phenotype of astrocytes in prion diseases can be sustained by reactive microglia and self-reinforced in a cell-autonomous manner. Our work highlights the pivotal role of Stat3 signaling in astrocyte activation and suggests that Stat3 inhibition may suppress the reactive phenotype of astrocytes associated with prion diseases.

Internal consistency, construct validity, and responsiveness of the MRC Prion Disease Rating Scale

BACKGROUND

The Medical Research Council-Prion Disease Rating Scale (MRC-PDRS) is a 20-point clinician-reported outcome scale to assess disease progression in patients with prion disease, an invariably fatal neurodegenerative disease caused by misfolded prion protein. This study aims to evaluate the measurement properties and interpretability of the MRC-PDRS to support the measure's use for effective disease management and research evaluating effectiveness of treatment options for prion diseases.

METHODOLOGY

Utilizing patient data from the Telemedicine Assessment Program for CJD (TAPCJD), statistical assessment was conducted of internal consistency, construct validity (including convergent, divergent validity, and known-groups discriminant validity), responsiveness, and interpretation guidelines using distribution-based approaches to estimate thresholds indicating minimal important change (MIC) in MRC-PDRS scores. Criterion measures used for evaluating construct validity and responsiveness included the Telephone Interview for Cognitive Status (TICS) and Neuropsychiatric Inventory-Questionnaire (NPI-Q).

RESULTS/CONCLUSIONS

These findings provide strong preliminary evidence that the MRC-PDRS is reliable, valid, and responsive as a tool for measuring disease progression in patients with prion disease, with preliminary MIC estimates ranging from 1 to 3 points. This supports the use of MRC-PDRS in evaluating potential treatment benefits of prion disease clinical trials, and potentially in clinical practice settings.

No structure, no problem: Protein stabilization by Hero proteins and other chaperone-like IDPs

In order for a protein to function, it must fold into its proper three-dimensional structure. Otherwise, improperly folded proteins are typically prone to aggregate through a process that is detrimental to cellular health. It is widely known that a diverse group of proteins, called molecular chaperones, function to promote proper folding of other proteins and prevent aggregation. In contrast, intrinsically disordered proteins (IDPs) lack substantial tertiary structures, but nonetheless serve important functional roles. In some cases, IDPs have been observed to display remarkably chaperone-like activities, where they stabilize the activities of client proteins and prevent their aggregation. While it was previously thought that chaperone-like IDPs were mainly utilized by extremophilic organisms in their survival of extreme stress, we recently showed that a group of chaperone-like IDPs, we named heat-resistant obscure (Hero) proteins, are also widespread in non-extremophile animals, including humans and flies. Thus, we should consider the possibility that IDPs serve significant chaperone-like functions in protein stabilization relevant to physiological conditions. However, as most of our understanding of how chaperones function is based on insights from their structured domains, it is unclear how chaperone-like IDPs elicit chaperone-like effects without these structures. Here we summarize our understanding of Hero proteins to date and, based on experimental evidence, outline the features that are likely important for their protein stabilizing activities. We draw on concepts from the studies of chaperones and chaperone-like IDPs, in order to draft potential models of how chaperone-like IDPs achieve chaperone-like effects in the absence of well-defined structures.

Hypothermia Shifts Neurodegeneration Phenotype in Neonatal Human Hypoxic-Ischemic Encephalopathy but Not in Related Piglet Models: Possible Relationship to Toxic Conformer and Intrinsically Disordered Prion-like Protein Accumulation

Hypothermia (HT) is used clinically for neonatal hypoxic-ischemic encephalopathy (HIE); however, the brain protection is incomplete and selective regional vulnerability and lifelong consequences remain. Refractory damage and impairment with HT cooling/rewarming could result from unchecked or altered persisting cell death and proteinopathy. We tested two hypotheses: (1) HT modifies neurodegeneration type, and (2) intrinsically disordered proteins (IDPs) and encephalopathy cause toxic conformer protein (TCP) proteinopathy neonatally. We studied postmortem human neonatal HIE cases with or without therapeutic HT, neonatal piglets subjected to global hypoxia-ischemia (HI) with and without HT or combinations of HI and quinolinic acid (QA) excitotoxicity surviving for 29-96 h to 14 days, and human oligodendrocytes and neurons exposed to QA for cell models. In human and piglet encephalopathies with normothermia, the neuropathology by hematoxylin and eosin staining was similar; necrotic cell degeneration predominated. With HT, neurodegeneration morphology shifted to apoptosis-necrosis hybrid and apoptotic forms in human HIE, while neurons in HI piglets were unshifting and protected robustly. Oligomers and putative TCPs of α-synuclein (αSyn), nitrated-Syn and aggregated αSyn, misfolded/oxidized superoxide dismutase-1 (SOD1), and prion protein (PrP) were detected with highly specific antibodies by immunohistochemistry, immunofluorescence, and immunoblotting. αSyn and SOD1 TCPs were seen in human HIE brains regardless of HT treatment. αSyn and SOD1 TCPs were detected as early as 29 h after injury in piglets and QA-injured human oligodendrocytes and neurons in culture. Cell immunophenotyping by immunofluorescence showed αSyn detected with antibodies to aggregated/oligomerized protein; nitrated-Syn accumulated in neurons, sometimes appearing as focal dendritic aggregations. Co-localization also showed aberrant αSyn accumulating in presynaptic terminals. Proteinase K-resistant PrP accumulated in ischemic Purkinje cells, and their target regions had PrP-positive neuritic plaque-like pathology. Immunofluorescence revealed misfolded/oxidized SOD1 in neurons, axons, astrocytes, and oligodendrocytes. HT attenuated TCP formation in piglets. We conclude that HT differentially affects brain damage in humans and piglets. HT shifts neuronal cell death to other forms in human while blocking ischemic necrosis in piglet for sustained protection. HI and excitotoxicity also acutely induce formation of TCPs and prion-like proteins from IDPs globally throughout the brain in gray matter and white matter. HT attenuates proteinopathy in piglets but seemingly not in humans. Shifting of cell death type and aberrant toxic protein formation could explain the selective system vulnerability, connectome spreading, and persistent damage seen in neonatal HIE leading to lifelong consequences even after HT treatment.

Iatrogenic Dementia: Providing Insight into Transmissible Subtype of Alzheimer's Disease, Creutzfeldt-Jakob Disease and Cerebral Amyloid Angiopathy

Within the phenotypic spectrum of Alzheimer's disease (AD), Creutzfeldt-Jakob disease (CJD) and cerebral amyloid angiopathy (CAA), dementia that is attributed to iatrogenic transmission has increasingly gained scientific attention recently. Newly recognized, this treatment-induced form of dementia may result from exposure to certain medical or surgical procedures. The present review aims to explore the distinct features of acquired dementia encompassing a history of potential exposure and relatively early age of onset, highlighting transmission potential with a rather prion-like pattern. Having reviewed all available relevant literature, dementia of iatrogenic etiology represents a new disease entity that requires an individualized investigation process and poses a great clinical challenge as far as patients with AD, CJD and CAA are concerned. Understanding the underlying pathophysiology of these rare forms of dementia may significantly enhance awareness within clinical field of neurodegenerative diseases and facilitate their prompt management.

Targeted protein degradation with bifunctional molecules as a novel therapeutic modality for Alzheimer's disease & beyond

Alzheimer's disease (AD) is associated with memory and cognitive impairment caused by progressive degeneration of neurons. The events leading to neuronal death are associated with the accumulation of aggregating proteins in neurons and glia of the affected brain regions, in particular extracellular deposition of amyloid plaques and intracellular formation of tau neurofibrillary tangles. Moreover, the accumulation of pathological tau proteoforms in the brain concurring with disease progression is a key feature of multiple neurodegenerative diseases, called tauopathies, like frontotemporal dementia (FTD) where autosomal dominant mutations in the tau encoding MAPT gene provide clear evidence of a causal role for tau dysfunction. Observations from disease models, post-mortem histology, and clinical evidence have demonstrated that pathological tau undergoes abnormal post-translational modifications, misfolding, oligomerization, changes in solubility, mislocalization, and intercellular spreading. Despite extensive research, there are few disease-modifying or preventative therapeutics for AD and none for other tauopathies. Challenges faced in tauopathy drug development include an insufficient understanding of pathogenic mechanisms of tau proteoforms, limited specificity of agents tested, and inadequate levels of brain exposure, altogether underscoring the need for innovative therapeutic modalities. In recent years, the development of experimental therapeutic modalities, such as targeted protein degradation (TPD) strategies, has shown significant and promising potential to promote the degradation of disease-causing proteins, thereby reducing accumulation and aggregation. Here, we review all modalities of TPD that have been developed to target tau in the context of AD and FTD, as well as other approaches that with innovation could be adapted for tau-specific TPD.

Detection and Decontamination of Chronic Wasting Disease Prions during Venison Processing

Prion diseases, including chronic wasting disease (CWD), are caused by prions, which are misfolded aggregates of normal cellular prion protein. Prions possess many characteristics that distinguish them from conventional pathogens, in particular, an extraordinary recalcitrance to inactivation and a propensity to avidly bind to surfaces. In middle to late stages of CWD, prions begin accumulating in cervid muscle tissues. Those features collectively create scenarios in which occupational hazards arise for workers processing venison and pose risks to consumers through direct prion exposure through ingestion and cross-contamination of food products. In this study, we demonstrate that steel and plastic surfaces used in venison processing can be directly contaminated with CWD prions and that cross-contamination of CWD-negative venison can occur from equipment that had previously been used with CWD-positive venison. We also show that several decontaminant solutions (commercial bleach and potassium peroxymonosulfate) are efficacious for prion inactivation on those same surfaces.

Investigating the Aggregation and Prionogenic Properties of Human Cancer-Related Proteins

Cancer encompasses a range of severe diseases characterized by uncontrolled cell growth and the potential for metastasis. Understanding the mechanism underlying tumorigenesis has been a central focus of cancer research. Self-propagating protein aggregates, known as prions, are linked to various biological functions and diseases, particularly those related to mammalian neurodegeneration. However, it remains unclear whether prion-like mechanisms contribute to tumorigenesis and cancer. Using a combined approach of algorithmic predictions, alongside genetic and biochemical experimentation, we identified numerous cancer-associated proteins prone to aggregation, many of which contain prion-like domains (PrLDs). These predictions were experimentally validated for both aggregation and prion-formation. We demonstrate that several PrLDs undergo nucleation-limited amyloid formation, which can alter protein activity in a mitotically heritable fashion. These include SSXT, a subunit of the chromatin-remodeling BAF (hSWI/SNF) complexes; CLOCK, a core component of the circadian clock; and EPN4, a clathrin-interacting protein involved in protein trafficking between the trans-Golgi network and endosomes. The prions formed by these PrLDs occurred in multiple variants and depended on Hsp104, a molecular chaperone with disaggregase activity. Our results reveal an inherent tendency for prion-like aggregation in human cancer-associated proteins, suggesting a potential role for such aggregation in the epigenetic changes driving tumorigenesis.

The Transformation Experiment of Frederick Griffith I: Its Narrowing and Potential for the Creation of Novel Microorganisms

The construction of artificial microorganisms often relies on the transfer of genomes from donor to acceptor cells. This synthetic biology approach has been considerably fostered by the J. Craig Venter Institute but apparently depends on the use of microorganisms, which are very closely related. One reason for this limitation of the "creative potential" of "classical" transformation is the requirement for adequate "fitting" of newly synthesized polypeptide components, directed by the donor genome, to interacting counterparts encoded by the pre-existing acceptor genome. Transformation was introduced in 1928 by Frederick Griffith in the course of the demonstration of the instability of pneumococci and their conversion from rough, non-pathogenic into smooth, virulent variants. Subsequently, this method turned out to be critical for the identification of DNA as the sole matter of inheritance. Importantly, the initial experimental design (1.0) also considered the inheritance of both structural (e.g., plasma membranes) and cybernetic information (e.g., metabolite fluxes), which, in cooperation, determine topological and cellular heredity, as well as fusion and blending of bacterial cells. In contrast, subsequent experimental designs (1.X) were focused on the use of whole-cell homogenates and, thereafter, of soluble and water-clear fractions deprived of all information and macromolecules other than those directing protein synthesis, including outer-membrane vesicles, bacterial prions, lipopolysaccharides, lipoproteins, cytoskeletal elements, and complexes thereof. Identification of the reasons for this narrowing may be helpful in understanding the potential of transformation for the creation of novel microorganisms.

Crosstalk Between Phase-Separated Membraneless Condensates and Membrane-Bound Organelles in Cellular Function and Disease

Compartmentalization in eukaryotic cells allows the spatiotemporal regulation of biochemical processes, in addition to allowing specific sets of proteins to interact in a regulated as well as stochastic manner. Although membrane-bound organelles are thought to be the key players of cellular compartmentalization, membraneless biomolecular condensates such as stress granules, P bodies, and many others have recently emerged as key players that are also thought to bring order to a highly chaotic environment. Here, we have evaluated the latest studies on biomolecular condensates, specifically focusing on how they interact with membrane-bound organelles and modulate each other's functions. We also highlight the importance of this interaction in neurodegenerative and cardiovascular diseases as well as in cancer.

Search for a genetic cause of variably protease-sensitive prionopathy

Variably protease-sensitive prionopathy (VPSPr) is a rare, atypical subtype of prion disease currently classified as sporadic. We performed exome sequencing and targeted sequencing of PRNP non-coding regions on genomic DNA from autopsy-confirmed VPSPr patients (N=67) in order to search for a possible genetic cause. Our search identified no potentially causal variants for VPSPr. The common polymorphism PRNP M129V was the largest genetic risk factor for VPSPr, with an odds ratio of 7.0. Other variants in and near PRNP exhibited association to VPSPr risk only in proportion to their linkage disequilibrium with M129V, and upstream expression quantitative trait loci showed no evidence of independent association to VPSPr risk. We cannot rule out the possibility of causal variants hiding in genomic regions or classes of genetic variation that our search did not canvas. Nevertheless, our data support the classification of VPSPr as a sporadic prion disease.

Chimerism: A whole new perspective in gene regulation

The diversity of molecular entities emerging from a single gene are recognized. Several studies have thus established the cellular role(s) of transcript variants and protein isoforms. A step ahead in challenging the central dogma towards expanding molecular diversity is the identification of fusion genes, chimeric transcripts and chimeric proteins that harbor sequences from more than one gene. The mechanisms for generation of chimeras largely follow similar patterns across all levels of gene regulation but also have interdependence and mutual exclusivity. Whole genome and RNA-seq technologies supported by development of computational algorithms and programs for processing datasets have increasingly enabled the identification of fusion genes and chimeric transcripts, while the discovery of chimeric proteins is as yet more subtle. Earlier thought to be associated with cellular transformation, the contribution of chimeric molecules to normal physiology is also realized and found to influence the expression of their parental genes and regulate cellular pathways. This review offers a collective and comprehensive overview of cellular chimeric entities encompassing the mechanisms involved in their generation, insights on their evolution, functions in gene regulation and their current and novel clinical applications.

Anti-Prion Systems in Saccharomyces cerevisiae

[PSI+] is a prion (infectious protein) of Sup35p, a subunit of the translation termination factor, and [URE3] is a prion of Ure2p, a mediator of nitrogen catabolite repression. Here, we trace the history of these prions and describe the array of anti-prion systems in S. cerevisiae. These systems work together to block prion infection, prion generation, prion propagation, prion segregation, and the lethal (and near-lethal) effects of most variants of these prions. Each system lowers the appearance of prions 2- to 15-fold, but together, ribosome-associated chaperones, the Hsp104 disaggregase, and the Sup35p-binding Upf proteins lower the frequency of [PSI+] appearance by ~5000-fold. [PSI+] variants can be categorized by their sensitivity to the various anti-prion systems, with the majority of prion isolates sensitive to all three of the above-mentioned systems. Yeast prions have been used to screen for human anti-prion proteins, and five of the Bag protein family members each have such activity. We suggest that manipulation of human anti-prion systems may be useful in preventing or treating some of the many human amyloidoses currently found to be prions with the same amyloid architecture as the yeast prions.

No evidence of subclinical infection in sheep surviving oral challenge with prions

Variant Creutzfeldt-Jakob disease (vCJD) is a fatal zoonotic disease caused by the ingestion of bovine spongiform encephalopathy (BSE)-infected meat products. Although the number of vCJD cases due to dietary exposure has significantly declined, the true burden of subclinical infections remains uncertain. Several large-scale surveys using appendix tissue samples have indicated the presence of abnormal prion protein (PrPSc; Sc for scrapie) in lymphoid tissue of a small proportion of the UK population. These may represent silent carriers of infection, with the potential to contribute to transmission, persistence and re-emergence of vCJD. Previously, we showed that subclinical infection is a frequent outcome of low-dose prion exposure by blood transfusion in sheep. To determine whether subclinical infection was also found following low-dose exposure by another clinically relevant route for humans, we screened archived tissues from sheep orally challenged with a range of doses of BSE, which did not show clinical or pathological signs of disease after several years of follow-up post-infection. Using a highly sensitive protein misfolding cyclic amplification assay, we were unable to detect PrPSc in the lymph node/tonsil of 15 sheep, or in a wider range of lymphoid tissues and brain (medulla oblongata) from a subset of 5 sheep. Our findings suggest that the route of infection/exposure may significantly influence the probability of establishing subclinical infection, with the oral route apparently much less efficient than intravenous infection by blood transfusion in sheep.

The Evolution of Experimental Rodent Models for Prion Diseases

Prion diseases are a group of fatal, neurodegenerative diseases that affect animals and humans. These diseases are characterized by the conformational conversion of normal, host-encoded PrPC into a disease-causing prion isoform, PrPSc. Significant advancements in biological, genetic, and prion research have led to the capability of studying this pathogenetic process using recombinant proteins, ex vivo systems, in vitro models, and mammalian hosts, the latter being the gold standard for assaying prion infectivity, transmission, and strain evolution. While devoid of nucleic acid, prions encipher strain information by the conformation of their constituent infectious proteins, with diversity altering pathogenesis, host-range dynamics, and the efficacy of therapeutics. To properly study the strain properties of natural prions and develop appropriate therapeutic strategies, it is essential to utilize models that authentically recapitulate these infectious agents in experimental mammalian hosts. In this review, we examine the evolution of research on prion diseases using non-transgenic and transgenic animals, primarily focusing on rodent models. We discuss the successes and limitations of each experimental system and provide insights based on recent findings in novel gene-targeted mice.

A novel ER stress regulator ARL6IP5 induces reticulophagy to ameliorate the prion burden

Prion disease is a fatal and infectious neurodegenerative disorder caused by the trans-conformation conversion of PRNP/PrPC to PRNP/PrPSc. Accumulated PRNP/PrPSc-induced ER stress causes chronic unfolded protein response (UPR) activation, which is one of the fundamental steps in prion disease progression. However, the role of various ER-resident proteins in prion-induced ER stress is elusive. This study demonstrated that ARL6IP5 is compensatory upregulated in response to chronically activated UPR in the cellular prion disease model (RML-ScN2a). Furthermore, overexpression of ARL6IP5 overcomes ER stress by lowering the expression of chronically activated UPR pathway proteins. We discovered that ARL6IP5 induces reticulophagy to reduce the PRNP/PrPSc burden by releasing ER stress. Conversely, the knockdown of ARL6IP5 leads to inefficient macroautophagic/autophagic flux and elevated PRNP/PrPSc burden. Our study also uncovered that ARL6IP5-induced reticulophagy depends on Ca2+-mediated AMPK activation and can induce 3 MA-inhibited autophagic flux. The detailed mechanistic study revealed that ARL6IP5-induced reticulophagy involves interaction with soluble reticulophagy receptor CALCOCO1 and lysosomal marker LAMP1, leading to degradation in lysosomes. Here, we delineate the role of ARL6IP5 as a novel ER stress regulator and reticulophagy inducer that can effectively reduce the misfolded PRNP/PrPSc burden. Our research opens up a new avenue of selective autophagy in prion disease and represents a potential therapeutic target.Abbreviations: ARL6IP5: ADP ribosylation factor-like GTPase 6 interacting protein 5; AMPK: adenosine 5'-monophosphate (AMP)-activated protein kinase; CALCOCO1: calcium binding and coiled-coil domain 1; CQ: chloroquine; DAPI: 4'6-diamino-2-phenylindole; ER: endoplasmic reticulum; ERPHS: reticulophagy/ER-phagy sites; KD: knockdown; KD-CON: knockdown control; LAMP1: lysosomal-associated membrane protein 1; MAP1LC3/LC3, microtubule-associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; MβCD: methyl beta cyclodextrin; 3 MA: 3-methyladenine; OE: overexpression; OE-CON: empty vector control; PrDs: prion diseases; PRNP/PrPC: cellular prion protein (Kanno blood group); PRNP/PrPSc: infectious scrapie misfolded PRNP; Tm: tunicamycin; UPR: unfolded protein response; UPS: ubiquitin-proteasome system.

Breaking the Mould: How the First Structure of a Deer Prion Suggests the Framework for Interspecies Strain Diversity and Transmission Barriers

Our Insight into the Structural Diversity of Prions Has Been Limited by Studies Focused on Rodent-Adapted Sheep (Scrapie) Prion Strains, Until Now. In a Recent Paper (Alam et al. 2024), the Caughey Research Group Presents the First Prion Structure from a Naturally Occurring Chronic Wasting Disease (CWD), Offering a Fresh Perspective.

Phylogeny and Molecular Characterisation of PRNP in Red-Tailed Phascogale (Phascogale calura)

Background/Objectives: The normal cellular prion protein (PrPC) is a cell-surface glycoprotein, mainly localised in neurons of the central nervous system (CNS). The human PRNP gene encodes 253 amino acid residues of precursor PrPC. Several studies that investigated the role of PRNP and PrPC in placental mammals, such as humans and mice, failed to reveal its exact function. Methods: In this study, we sequenced and characterised the PRNP gene and PrPC of the marsupial, P. calura, as a strategy to gain molecular insights into its structure and physicochemical properties. Placentals are separated from marsupials by approximately 125 million years of independent evolution. Results: Standard Western blotting analysis of PrPC phascogale displayed the typical un-, mono-, and di-glycosylated bands recognized in placentals. Furthermore, we showed that phascogale PRNP gene has two exons, similar to all the marsupials and placentals of the PRNP genes studied. Of note, the phascogale PRNP gene contained distinctive repeats in the PrPC tail region comparable to the closely related Tasmanian devil (Sarcophilus harrisii) and more distantly related to the grey short-tailed opossum (Monodelphis domestica), common wombat (Vombatus ursinus), and Tammar wallaby (Macropus eugenii); however, its specific composition and numbers were different from placentals. Of importance, comparisons of the phascogale's PrPC physicochemical properties with other monotremes, marsupials, and placentals confirmed the Monotremata-Marsupialia-Placentalia evolutionary distance. We found that the protein instability index, a method used to predict the stability of a protein in vivo (Stable: <40; Instable >40), showed that the PrPC of all marsupials tested, including phascogale, were highly stable compared with the birds, reptiles, amphibians, and fish that were shown to be highly unstable. However, the instability index predicted that all placental species, including human (Homo sapiens), mouse (Mus musculus), bank vole (Myodes glareolus), rhinoceros (Rhinocerotidae), dog (Canis lupus familiaris), flying fox (Pteropus vampyrus), whale (Physeter catodon), cattle (Bos taurus), and sheep (Ovis aries), were either slightly unstable or nearly unstable. Further, our analysis revealed that despite their predicted high PrPC stability, P. calura exhibited substantial N-terminal disorder (53.76%), while species with highly unstable PrPCs based on their instability index, such as Danio rerio, Oryzias latipes, and Astyanax mexicanus, displayed even higher levels of N-terminal disorder (up to 75.84%). These findings highlight a discrepancy between overall predicted stability and N-terminal disorder, suggesting a potential compensatory role of disorder in modulating prion protein stability and function. Conclusions: These results suggest that the high stability of marsupial prion proteins indicates a vital role in maintaining protein homeostasis; however more work is warranted to further depict the exact function.

Detection of chronic wasting disease prions in the farm soil of the Republic of Korea

Chronic wasting disease (CWD) is a highly contagious prion disease occurring in free-ranging and farmed cervids. CWD continues to spread uncontrolled across North America, and cases continue to be detected almost every year in the Republic of Korea. CWD-infected animals contaminate the soil by releasing infectious prions through their excreta, and shed prions accumulate and remain infectious in the soil for years. Given that the upper soil levels can become contaminated with prions and serve as infectivity reservoirs facilitating horizontal transmission of CWD, the ability to detect prions in the soil is needed for monitoring and managing CWD spread. Using the protein misfolding cyclic amplification (PMCA) technique, we investigated whether prions could be amplified and detected in farm soil experimentally exposed to CWD-infected brain homogenate as well as in the soil of CWD-affected farms. From each soil sample, we performed 10 serial extractions and used these 10 extracts as PMCA templates. Here, we show that prion seeding activity was detected in extracts from farm soil following 4 years of incubation with CWD-infected brain homogenate. More importantly, 13 of 38 soil samples collected from six CWD-affected farms displayed prion seeding activity, with at least one soil sample in each farm being PMCA positive. Mouse bioassays confirmed the presence of prion infectivity in the soil extracts in which PMCA seeding activity was detected. This is the first report describing the successful detection of prions in soil collected from CWD-affected farms, suggesting that PMCA conducted on serial soil extracts is a sensitive means for prion detection in CWD-contaminated soil.IMPORTANCEChronic wasting disease (CWD) is a highly contagious prion disease affecting free-ranging and farmed cervids. CWD continues to spread uncontrollably across North America, and multiple cases are detected annually in the Republic of Korea. Prions shed from CWD-infected animals remain infectious in the soil for years, serving as infectivity reservoirs that facilitate horizontal transmission of the disease. Therefore, the ability to detect CWD prions in soil is crucial for monitoring and managing the spread of the disease. In this study, we have demonstrated for the first time that prions in the soil of CWD-affected farms can be reliably detected using a combination of serial soil extraction and a prion amplification technique. Our data, in which at least one soil sample tested positive for CWD in each of the six CWD-affected farms analyzed, suggest that the approach employed in this study is a sensitive method for prion detection in CWD-contaminated soil.

Exploring the Potential Interaction between the Functional Prion Protein CPEB3 and the Amyloidogenic Pathogenic Protein Tau

Abnormal aggregation of tau protein is pathologically linked to Alzheimer's disease, while the aggregation of the prion-like RNA-binding protein (RBP) CPEB3 is functional and is associated with long-term memory. However, the interaction between these two memory-related proteins has not yet been explored. Our residue-specific NMR relaxation study revealed that the first prion domain of CPEB3 (PRD1) interacts with the 306VQIVYKPVDLSKV318 segment of tau and prevents the aggregation of tau-K18. Notably, this interaction is synergistic as it not only inhibits tau-K18 aggregation but also enhances PRD1 fibril formation. We also studied the interaction of different PRD1 subdomains with tau-K18 to elucidate the precise region of PRD1 that inhibits tau-K18 aggregation. This revealed that the PRD1-Q region is responsible for preventing tau-K18 aggregation. Inspired by this, we synthesized a 15 amino acid Poly-Q peptide that inhibits tau-K18 aggregation, suggesting its potential as a small drug-like molecule for Alzheimer's disease therapeutics.

Distinct patterns of prion strain deposition and toxicity in a novel whole brain organotypic slice culture system

Prion diseases are fatal transmissible neurodegenerative diseases that affect many mammals, including humans, caused by the templated misfolding of the prion protein. Different conformations of misfolded prions can occur, leading to distinct disease phenotypes or strains and the accumulation of prions in distinct brain regions. How prion structure influences this brain tropism is not clear, but the transmissible nature of prion diseases has allowed for the development of ex vivo brain slice models of disease. To date, work has been done in cerebellar cultures, but prion diseases are known to differentially affect many other brain regions. We have adapted this approach to a coronally sliced whole brain organotypic culture and demonstrate distinct profiles of cytotoxicity and neuronal loss upon exposure to four mouse-adapted scrapie strains. We were able to induce infection both diffusely through submersion of slice cultures in infectious media and locally through contact with prion-coated stainless-steel wires. Moreover, we observed consistent strain-specific regional differences in prion deposition by 8 weeks of infection, recapitulating what is seen in vivo. We predict that coronal whole brain organotypic slice cultures can be a powerful tool for elucidating strain-specific mechanisms of prion spread and pathology.

β-synuclein in cerebrospinal fluid as a potential biomarker for distinguishing human prion diseases from Alzheimer's and Parkinson's disease

BACKGROUND

β-synuclein (β-syn), mainly expressed in central nerve system, is one of the biomarkers in cerebrospinal fluid (CSF) and blood for synaptic damage, which has been reported to be elevated in CSF and blood of the patients of prion diseases (PrDs).

METHODS

We analyzed 314 CSF samples from patients in China National Surveillance for CJD. The diagnostic groups of the 223 patients with PrDs included sporadic Creutzfeldt-Jacob disease (sCJD), genetic CJD (gCJD), fatal familial insomnia (FFI) and Gerstmann-Straussler-Scheinker (GSS). 91 patients with non-PrDs comprised Alzheimer's disease (AD), Parkinson's disease (PD), viral encephalitis (VE) or autoimmune encephalitis (AE) were enrolled in the control groups. The CSF β-syn levels were measured by a commercial microfluidic ELISA. The Mann-Whitney U test and Kruskal-Wallis H test were employed to analyze two or more sets of continuous variables. Multiple linear regression was also performed to evaluate the factors for CSF β-syn levels. Receiver operating characteristics (ROC) curves and area under the curve (AUC) values were used to assess the diagnostic performance of β-syn.

RESULTS

The median of β-syn levels (2074 pg/ml; IQR: 691 to 4332) of all PrDs was significantly higher than that of non-PrDs group (504 pg/ml; IQR: 126 to 3374). The CSF β-syn values in the cohorts of sCJD, T188K-gCJD, E200K-gCJD and P102L-GSS were remarkably higher than that of the group of AD + PD, but similar as that of the group of VE + AE. The elevated CSF β-syn in sCJD and gCJD cases was statistically associated with CSF 14-3-3 positive and appearance of mutism. ROC curve analysis identified satisfied performance for distinguishing from AD + PD, with high AUC values in sCJD (0.7640), T188K-gCJD (0.8489), E200K-gCJD (0.8548), P102L-GSS (0.7689) and D178N-FFI (0.7210), respectively.

CONCLUSION

Our data here indicate that CSF β-syn is a potential biomarker for distinguishing PrDs (gCJD, sCJD and GSS) from AD and PD, but is much less efficient from VE and AE. These findings have critical implications for early diagnosis and monitoring of synaptic integrity in prion diseases.

NIR Light-Triggered Structural Modulation of Self-Assembled Prion Protein Aggregates

The self-replication of misfolded prion protein (PrP) aggregates is the major pathological event of different prion diseases, affecting mammal brains by cross-species transmission. Here, the structural modulation of PrP aggregates are reported by activated carbon materials upon near-infrared (NIR) light irradiation. Activated carbon cobalt (ACC) nanosheets are synthesized using glycerol and metal salts to utilize the charge carriers released under NIR light exposure. According to the microscopy and spectroscopy analysis results, NIR light-excited ACC nanosheets successfully dissociate the β-sheet-rich and plaque-like PrP aggregates into denatured fragments by modifying their amino acid residues. The in vitro assay results demonstrate that ACC nanosheets possess biocompatibility to neuroblastoma cells and alleviating effect against the neurotoxicity of PrP aggregates. This work suggests the first potential photodynamic platform for the future treatment of prion diseases.

Prions in Muscles of Cervids with Chronic Wasting Disease, Norway

Chronic wasting disease (CWD) is an emerging prion disease in Nordic countries and has been detected in reindeer, moose, and red deer since 2016. CWD sporadically detected in moose and red deer in 3 Nordic countries demonstrated pathologic and strain characteristics different from CWD in reindeer, including an unexpected lack of prions outside the central nervous system as measured by standard diagnostic tests. Using protein misfolding cyclic amplification, we detected prions in the lymphoreticular system of moose and red deer with CWD in Norway and, remarkably, in muscles of both of those species and in CWD-infected reindeer. One moose lymph node and 1 moose muscle sample showed infectivity when experimentally transmitted to bank voles. Our findings highlight the systemic nature of CWD strains in Europe and raise questions regarding the risk of human exposure through edible tissues.

Exploring immunotherapeutic strategies for neurodegenerative diseases: a focus on Huntington's disease and Prion diseases

Immunotherapy has emerged as a promising therapeutic approach for the treatment of neurodegenerative disorders, which are characterized by the progressive loss of neurons and impaired cognitive functions. In this review, active and passive immunotherapeutic strategies that help address the underlying pathophysiology of Huntington's disease (HD) and prion diseases by modulating the immune system are discussed. The current landscape of immunotherapeutic strategies, including monoclonal antibodies and vaccine-based approaches, to treat these diseases is highlighted, along with their potential benefits and mechanisms of action. Immunotherapy generally works by targeting disease-specific proteins, which serve as the pathological hallmarks of these diseases. Additionally, the review addresses the challenges and limitations associated with immunotherapy. For HD, immunotherapeutic approaches focus on neutralizing the toxic effects of mutant huntingtin and tau proteins, thereby reducing neurotoxicity. Immunotherapeutic approaches targeting flanking sequences, rather than the polyglutamine tract in the mutant huntingtin protein, have yielded promising outcomes for patients with HD. In prion diseases, therapies attempt to prevent or eliminate misfolded proteins that cause neurodegeneration. The major challenge in prion diseases is immune tolerance. Approaches to overcome the highly tolerogenic nature of the prion protein have been discussed. A common hurdle in delivering antibodies is the blood‒brain barrier, and strategies that can breach this barrier are being investigated. As protein aggregation and neurotoxicity are related, immunotherapeutic strategies being developed for other neurodegenerative diseases could be repurposed to target protein aggregation in HD and prion diseases. While significant advances in this field have been achieved, continued research and development are necessary to overcome the existing limitations, which will help in shaping the future of immunotherapy as a strategy for managing neurological disorders.

Comparing the Extent of Methionine Oxidation in the Prion and Native Conformations of PrP

Scrapie is a prion disease of sheep and goats. Prions (PrPSc) replicate by inducing a natively expressed protein (PrPC) to refold into the prion conformation. PrPC and PrPSc contain a disproportionately large number of methionines. Surface exposed methionines are more prone to chemical oxidation. Chemical oxidation is a means of measuring the surface exposure of the methionines in a prion, as these covalent changes are retained after an oxidized prion is denatured prior to analysis. Scrapie prions and recombinant sheep prion protein were oxidized in 0, 10, 20, or 50 mM solutions of hydrogen peroxide. The samples were digested with trypsin or trypsin followed by chymotrypsin to yield a set of peptides (TNMK, MLGSAMSR, ENMYR, IMER, VVEQMCITQYQR) containing the methionines present in sheep PrP. The mass spectrometry based multiple reaction monitoring (MRM) method was used to analyze these peptides. Analysis of the rPrP samples showed that surface exposed methionines (132, 137, and 157) were more oxidized than those less surface exposed (209 and 216). The extent of methionine oxidation in sheep scrapie PrPSc is 216 > 137 > 132 > 157 > 209 > 112. These results demonstrate that this approach can be used to map the surface exposure of the methionines in order to distinguish among PrP conformations and effect a kind of conformational sequence.

CRISPR/Cas9-editing of PRNP in Alpine goats

Misfolding of the cellular PrP (PrPc) protein causes prion disease, leading to neurodegenerative disorders in numerous mammalian species, including goats. A lack of PrPc induces complete resistance to prion disease. The aim of this work was to engineer Alpine goats carrying knockout (KO) alleles of PRNP, the PrPc-encoding gene, using CRISPR/Cas9-ribonucleoproteins and single-stranded donor oligonucleotides. The targeted region preceded the PRNPTer mutation previously described in Norwegian goats. Genome editors were injected under the zona pellucida prior to the electroporation of 565 Alpine goat embryos/oocytes. A total of 122 two-cell-stage embryos were transferred to 46 hormonally synchronized recipient goats. Six of the goats remained pregnant and naturally gave birth to 10 offspring. Among the 10 newborns, eight founder animals carrying PRNP genome-edited alleles were obtained. Eight different mutated alleles were observed, including five inducing KO mutations. Three founders carried only genome-edited alleles and were phenotypically indistinguishable from their wild-type counterparts. Among them, one male carrying a one base pair insertion leading to a KO allele is currently used to rapidly extend a PRNP-KO line of Alpine goats for future characterization. In addition to KO alleles, a PRNPdel6 genetic variant has been identified in one-third of founder animals. This new variant will be tested for its potential properties with respect to prion disease. Future studies will also evaluate the effects of genetic background on other characters associated with PRNP KO, as previously described in the Norwegian breed or other species.

Evaluation of RT-QuIC Diagnostic Performance for Chronic Wasting Disease Detection Using Elk (Cervus canadensis) Ear Punches

Sensitive and specific antemortem diagnostic tests are a prerequisite for effective management of chronic wasting disease (CWD). Paired with readily accessible samples that accurately reflect CWD status, the real-time quaking-induced conversion (RT-QuIC) assay has the potential to enable more effective CWD surveillance and interventions. We evaluated the feasibility of RT-QuIC as a CWD diagnostic test using 6-mm ear tissue biopsies from elk (Cervus canadensis). First, we evaluated the effect of ear spatial location on seeding activity. We observed an effect of ear punch spatial location on the amyloid formation rate (AFR): Samples collected from the periphery of the ear evidenced a statistically significant increase in AFR relative to ear punches from the ventral midline. Gross microdissection of an ear pinna suggested that there was more small nerve innervation around the periphery of the ear. Second, we evaluated the diagnostic sensitivity, specificity, and predictive value of RT-QuIC using ear punches from elk that had been previously diagnosed via ELISA testing. We evaluated the impact of nonstatistical and statistical approaches on diagnostic accuracy. Specificity and positive predictive value were perfect when statistical analyses were used to evaluate the binomial distribution (CWD positive versus CWD negative) of the data. Conversely, sensitivity and negative predictive value were modest, independent of the application of statistical analysis, indicating that RT-QuIC may be susceptible to false-negative data in this context. Taken together, our data support the idea that RT-QuIC, when paired with US Department of Agriculture-approved diagnostic tests, may provide more time to stakeholders for making major management decisions.

Comparing Prion Proteins Across Species: Is Zebrafish a Useful Model?

Despite the considerable body of research dedicated to the field of neurodegeneration, the gap in knowledge on the prion protein and its intricate involvement in brain diseases remains substantial. However, in the past decades, many steps forward have been taken toward a better understanding of the molecular mechanisms underlying both the physiological role of the prion protein and the misfolding event converting it into its pathological counterpart, the prion. This review aims to provide an overview of the main findings regarding this protein, highlighting the advantages of many different animal models that share a conserved amino acid sequence and/or structure with the human prion protein. A particular focus will be given to the species Danio rerio, a compelling research organism for the investigation of prion biology, thanks to its conserved orthologs, ease of genetic manipulation, and cost-effectiveness of high-throughput experimentation. We will explore its potential in filling some of the gaps on physiological and pathological aspects of the prion protein, with the aim of directing the future development of therapeutic interventions.

Prion Protein Endoproteolysis: Cleavage Sites, Mechanisms and Connections to Prion Disease

Highly abundant in neurons, the cellular prion protein (PrPC) is an obligatory precursor to the disease-associated misfolded isoform denoted PrPSc that accumulates in the rare neurodegenerative disorders referred to either as transmissible spongiform encephalopathies (TSEs) or as prion diseases. The ability of PrPC to serve as a substrate for this template-mediated conversion process depends on several criteria but importantly includes the presence or absence of certain endoproteolytic events performed at the cell surface or in acidic endolysosomal compartments. The major endoproteolytic events affecting PrPC are referred to as α- and β-cleavages, and in this review we outline the sites within PrPC at which the cleavages occur, the mechanisms potentially responsible and their relevance to pathology. Although the association of α-cleavage with neuroprotection is well-supported, we identify open questions regarding the importance of β-cleavage in TSEs and suggest experimental approaches that could provide clarification. We also combine findings from in vitro cleavage assays and mass spectrometry-based studies of prion protein fragments in the brain to present an updated view in which α- and β-cleavages may represent two distinct clusters of proteolytic events that occur at multiple neighbouring sites rather than at single positions. Furthermore, we highlight the candidate proteolytic mechanisms best supported by the literature; currently, despite several proteases identified as capable of processing PrPC in vitro, in cell-based models and in some cases, in vivo, none have been shown conclusively to cleave PrPC in the brain. Addressing this knowledge gap will be crucial for developing therapeutic interventions to drive PrPC endoproteolysis in a neuroprotective direction. Finally, we end this review by briefly addressing other cleavage events, specifically ectodomain shedding, γ-cleavage, the generation of atypical pathological fragments in the familial prion disorder Gerstmann-Sträussler-Scheinker syndrome and the possibility of an additional form of endoproteolysis close to the PrPC N-terminus.

Cofactors facilitate bona fide prion misfolding in vitro but are not necessary for the infectivity of recombinant murine prions

Prion diseases, particularly sporadic cases, pose a challenge due to their complex nature and heterogeneity. The underlying mechanism of the spontaneous conversion from PrPC to PrPSc, the hallmark of prion diseases, remains elusive. To shed light on this process and the involvement of cofactors, we have developed an in vitro system that faithfully mimics spontaneous prion misfolding using minimal components. By employing this PMSA methodology and introducing an isoleucine residue at position 108 in mouse PrP, we successfully generated recombinant murine prion strains with distinct biochemical and biological properties. Our study aimed to explore the influence of a polyanionic cofactor in modulating strain selection and infectivity in de novo-generated synthetic prions. These results not only validate PMSA as a robust method for generating diverse bona fide recombinant prions but also emphasize the significance of cofactors in shaping specific prion conformers capable of crossing species barriers. Interestingly, once these conformers are established, our findings suggest that cofactors are not necessary for their infectivity. This research provides valuable insights into the propagation and maintenance of the pathobiological features of cross-species transmissible recombinant murine prion and highlights the intricate interplay between cofactors and prion strain characteristics.

The dynamics of prion spreading is governed by the interplay between the non-linearities of tissue response and replication kinetics

Prion diseases, or transmissible spongiform encephalopathies (TSEs), are neurodegenerative disorders caused by the accumulation of misfolded conformers (PrPSc) of the cellular prion protein (PrPC). During the pathogenesis, the PrPSc seeds disseminate in the central nervous system and convert PrPC leading to the formation of insoluble assemblies. As for conventional infectious diseases, variations in the clinical manifestation define a specific prion strain which correspond to different PrPSc structures. In this work, we implemented the recent developments on PrPSc structural diversity and tissue response to prion replication into a stochastic reaction-diffusion model using an application of the Gillespie algorithm. We showed that this combination of non-linearities can lead prion propagation to behave as a complex system, providing an alternative to the current paradigm to explain strain-specific phenotypes, tissue tropisms, and strain co-propagation while also clarifying the role of the connectome in the neuro-invasion process.

[SNG2], a prion form of Cut4/Apc1, confers non-Mendelian inheritance of heterochromatin silencing defect in fission yeast

Prions represent epigenetic regulator proteins that can self-propagate their structure and confer their misfolded structure and function on normally folded proteins. Like the mammalian prion PrPSc, prions also occur in fungi. While a few prions, like Swi1, affect gene expression, none are shown to affect heterochromatin structure and function. In fission yeast and metazoans, histone methyltransferase Clr4/Suv39 causes H3-Lys9 methylation, which is bound by the chromodomain protein Swi6/HP1 to assemble heterochromatin. Earlier, we showed that sng2-1 mutation in the Cut4 subunit of anaphase-promoting complex abrogates heterochromatin structure due to defective binding and recruitment of Swi6. Here, we demonstrate that the Cut4p forms a non-canonical prion form, designated as [SNG2], which abrogates heterochromatin silencing. [SNG2] exhibits various prion-like properties, e.g. non-Mendelian inheritance, requirement of Hsp proteins for its propagation, de novo generation upon cut4 overexpression, reversible curing by guanidine, cytoplasmic inheritance and formation of infectious protein aggregates, which are dissolved upon overexpression of hsp genes. Interestingly, [SNG2] prion imparts an enhanced tolerance to stress conditions, supporting its role in promoting cell survival under environmental stress during evolution.

[PSI]-CIC: A Deep-Learning Pipeline for the Annotation of Sectored Saccharomyces cerevisiae Colonies

The [ P S I + ] prion phenotype in yeast manifests as a white, pink, or red color pigment. Experimental manipulations destabilize prion phenotypes, and allow colonies to exhibit [ p s i - ] (red) sectored phenotypes within otherwise completely white colonies. Further investigation of the size and frequency of sectors that emerge as a result of experimental manipulation is capable of providing critical information on mechanisms of prion curing, but we lack a way to reliably extract this information. Images of experimental colonies exhibiting sectored phenotypes offer an abundance of data to help uncover molecular mechanisms of sectoring, yet the structure of sectored colonies is ignored in traditional biological pipelines. In this study, we present [PSI]-CIC, the first computational pipeline designed to identify and characterize features of sectored yeast colonies. To overcome the barrier of a lack of manually annotated data of colonies, we develop a neural network architecture that we train on synthetic images of colonies and apply to real images of [ P S I + ] , [ p s i - ] , and sectored colonies. In hand-annotated experimental images, our pipeline correctly predicts the state of approximately 95% of colonies detected and frequency of sectors in approximately 89.5% of colonies detected. The scope of our pipeline could be extended to categorizing colonies grown under different experimental conditions, allowing for more meaningful and detailed comparisons between experiments. Our approach streamlines the analysis of sectored yeast colonies providing a rich set of quantitative metrics and provides insight into mechanisms driving the curing of prion phenotypes.

The Aggravating Role of Failing Neuropeptide Networks in the Development of Sporadic Alzheimer's Disease

Alzheimer's disease imposes an increasing burden on aging Western societies. The disorder most frequently appears in its sporadic form, which can be caused by environmental and polygenic factors or monogenic conditions of incomplete penetrance. According to the authors, in the majority of cases, Alzheimer's disease represents an aggravated form of the natural aging of the central nervous system. It can be characterized by the decreased elimination of amyloid β1-42 and the concomitant accumulation of degradation-resistant amyloid plaques. In the present paper, the dysfunction of neuropeptide regulators, which contributes to the pathophysiologic acceleration of senile dementia, is reviewed. However, in the present review, exclusively those neuropeptides or neuropeptide families are scrutinized, and the authors' investigations into their physiologic and pathophysiologic activities have made significant contributions to the literature. Therefore, the pathophysiologic role of orexins, neuromedins, RFamides, corticotrope-releasing hormone family, growth hormone-releasing hormone, gonadotropin-releasing hormone, ghrelin, apelin, and natriuretic peptides are discussed in detail. Finally, the therapeutic potential of neuropeptide antagonists and agonists in the inhibition of disease progression is discussed here.

Rigidifying the β2-α2 Loop in the Mouse Prion Protein Slows down Formation of Misfolded Oligomers

Transmissible Spongiform Encephalopathies are fatal neurodegenerative diseases caused by the misfolding of the cellular prion protein (PrPC) into its pathological isoform (PrPSc). Efficient transmission of PrPSc occurs within the same species, but a species barrier limits interspecies transmission. While PrP structure is largely conserved among mammals, variations at the β2-α2 loop are observed, and even minor changes in the amino acid sequence of the β2-α2 loop can significantly affect transmission efficiency. The present study shows that the introduction of the elk/deer-specific amino acid substitutions at positions 169 (Ser to Asn) and 173 (Asn to Thr) into the mouse prion protein, which are associated with the structural rigidity of the β2-α2 loop, has a substantial impact on protein dynamics as well as on the misfolding pathways of the protein. Native state hydrogen-deuterium exchange studies coupled with mass spectrometry, show that the rigid loop substitutions stabilize not only the β2-α2 loop but also the C-terminal end of α3, suggesting that molecular interactions between these two segments are strengthened. Moreover, the energy difference between the native state and multiple misfolding-prone partially unfolded forms (PUFs) present at equilibrium, is increased. The decreased accessibility of the PUFs from the native state leads to a slowing down of the misfolding of the protein. The results of this study provide important insights into the early events of conformational conversion of prion protein into β-rich oligomers, and add to the evidence that the β2-α2 loop is a key determinant in prion protein aggregation.

Prion meeting 2023: implications of a growing field

The history of human prion diseases began with the original description, by Hans Gerhard Creutzfeldt and by Alfons Maria Jakob, of patients with a severe brain disease that included speech abnormalities, confusion, and myoclonus, in a disease that was then named Creutzfeldt Jakob disease (CJD). Later, in Papua New Guinea, a disease characterized by trembling was identified, and given the name "Kuru". Neuropathological examination of the brains from CJD and Kuru patients, and of brains of sheep with scrapie disease revealed significant similarities and suggested a possible common mode of infection that, at the time, was thought to derive from an unknown virus that caused slow infections. John Stanley Griffith hypothesized that the agent causing these diseases was "probably a protein without nucleic acid" and, in 1982, Stanley Prusiner reported the identification of a proteinaceous infectious particle (coining the term prion) that was resistant to inactivation methods that were at the time standard for nucleic acids, and identified PrP as the major protein component of the infectious agent in scrapie and in Creutzfeldt-Jakob disease, classifying this also as a prion disease. Interestingly, the prion concept had been previously expanded to yeast proteins capable of replicating their conformation, seeding their own aggregation and transmitting phenotypic information. The prion concept has been more recently expanded to refer to misfolded proteins that are capable of converting a normal form of a protein into an abnormal form. The quest to understand and treat prion diseases has united a specific research community around the topic, and regular meetings (Prion Meetings) have taken place over the years to enable discussions, train junior researchers, and inspire research in the field.

Prion forensics: a multidisciplinary approach to investigate CWD at an illegal deer carcass disposal site

Infectious prions are resistant to degradation and remain infectious in the environment for several years. Chronic wasting disease (CWD) has been detected in cervids inhabiting North America, the Nordic countries, and South Korea. CWD-prion spread is partially attributed to carcass transport and disposal. We employed a forensic approach to investigate an illegal carcass dump site connected with a CWD-positive herd. We integrated anatomic, genetic, and prion amplification methods to discover CWD-positive remains from six white-tailed deer (Odocoileus virginianus) and, using microsatellite markers, confirmed a portion originated from the CWD-infected herd. This approach provides a foundation for future studies of carcass prion transmission risk.

Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation

Protein aggregation is responsible for several degenerative conditions in humans, and it is also a bottleneck in industrial protein production and storage of biotherapeutics. Bioinformatics tools have been developed to predict and redesign protein solubility more efficiently by understanding the underlying principles behind aggregation. As more experimental data become available, dedicated resources for storing, indexing, classifying and consolidating experimental results have emerged. These resources vary in focus, including aggregation-prone regions, 3D patches or protein stretches capable of forming amyloid fibrils. Some of these resources also consider the experimental conditions that cause protein aggregation and how they affect the process. This review article explores how protein aggregation databases have evolved and surveys state-of-the-art resources. We highlight their applications, complementarity and existing limitations. Moreover, we showcase the existing symbiosis between amyloid-related databases and predictive tools. To increase the usefulness of our review, we supplement it with a comprehensive list of present and past amyloid databases: https://biogenies.info/amyloid-database-list/.

A review of chronic wasting disease (CWD) spread, surveillance, and control in the United States captive cervid industry

Chronic wasting disease (CWD) is a fatal prion disease of the family Cervidae that circulates in both wild and captive cervid populations. This disease threatens the health and economic viability of the captive cervid industry, which raises cervids in contained spaces for purposes such as hunting and breeding. Given the high transmissibility and long incubation period of CWD, the introduction and propagation of the infectious prion protein within and between captive cervid farms could be devastating to individual facilities and to the industry as a whole. Despite this risk, there does not yet exist a literature review that summarizes the scientific knowledge, to date, about CWD spread, surveillance, or control measures. Our review, which focused on peer reviewed, primary research conducted in the United States, sought to address this need by searching Google Scholar, Scopus, and Web of Science with a five-term keyword string containing terms related to the (1) location, (2) species affected, (3) disease, (4) captive cervid industry, and (5) topic of focus. Between the three databases, there were 190 articles that were selected for further examination. Those articles were then read to determine if they were about CWD spread, surveillance, and/or control in captive cervid facilities. The 22 articles that met these inclusion criteria were evaluated in detail and discussed, with recommendations for future collaborative work between captive cervid owners, government agencies, and researchers. This work will help to address, inform, and mitigate the rising problem of CWD spread and establishment.

The importance of prion research

Over the past four decades, prion diseases have received considerable research attention owing to their potential to be transmitted within and across species as well as their consequences for human and animal health. The unprecedented nature of prions has led to the discovery of a paradigm of templated protein misfolding that underlies a diverse range of both disease-related and normal biological processes. Indeed, the "prion-like" misfolding and propagation of protein aggregates is now recognized as a common underlying disease mechanism in human neurodegenerative disorders such as Alzheimer's and Parkinson's disease, and the prion principle has led to the development of novel diagnostic and therapeutic strategies for these illnesses. Despite these advances, research into the fundamental biology of prion diseases has declined, likely due to their rarity and the absence of an acute human health crisis. Given the past translational influence, continued research on the etiology, pathogenesis, and transmission of prion disease should remain a priority. In this review, we highlight several important "unsolved mysteries" in the prion disease research field and how solving them may be crucial for the development of effective therapeutics, preventing future outbreaks of prion disease, and understanding the pathobiology of more common human neurodegenerative disorders.

New preclinical biomarkers for prion diseases in the cerebrospinal fluid proteome revealed by mass spectrometry

Current diagnostic methods for prion diseases only work in late stages of the disease when neurodegeneration is irreversible. Therefore, biomarkers that can detect the disease before the onset of clinical symptoms are necessary. High-throughput discovery proteomics is of great interest in the search for such molecules. Here we used mass spectrometry to analyse the cerebrospinal fluid proteome in an animal prion disease: preclinical and clinical sheep affected with natural scrapie, and healthy sheep. Interestingly, we found 46 proteins in the preclinical stage that were significantly altered (p < 0.01) compared to healthy sheep, mainly associated with biological processes such as stress and inflammatory responses. Five of them were selected for validation by enzyme-like immunosorbent assay: synaptotagmin binding, cytoplasmic RNA interacting protein (SYNCRIP), involved in nucleic acid metabolism; phospholipase D3 (PLD3) and cathepsin D (CTSD), both related to lysosomal apoptosis; complement component 4 (C4), an element of the classical immune response; and osteopontin (SPP1), a proinflammatory cytokine. These proteins significantly increased in the preclinical stage and maintained their levels in the clinical phase, except for CTSD, whose concentration returned to basal levels in the clinical group. Further research is ongoing to explore their potential as preclinical biomarkers of prion diseases.

Disease-Associated Q159X Mutant Prion Protein Is Sufficient to Cause Fatal Degenerative Disease in Mice

PRNP Q160X is one of the five dominantly inheritable nonsense mutations causing familial prion diseases. Till now, it remains unclear how this type of nonsense mutations causes familial prion diseases with unique clinical and pathological characteristics. Human prion protein (PrP) Q160X mutation is equivalent to Q159X in mouse PrP, which produces the mutant fragment PrP1-158. Through intracerebroventricular injection of recombinant adeno-associated virus in newborn mice, we successfully overexpressed mouse PrP1-158-FLAG in the central nervous system. Interestingly, high level PrP1-158-FLAG expression in the brain caused death in these mice with an average survival time of 60 ± 9.1 days. Toxicity correlated with levels of PrP1-158-FLAG but was independent of endogenous PrP. Histopathological analyses showed microgliosis and astrogliosis in mouse brains expressing PrP1-158-FLAG and most of PrP1-158-FLAG staining appeared intracellular. Biochemical characterization revealed that the majority of PrP1-158-FLAG were insoluble and a significant part of PrP1-158-FLAG appeared to contain an un-cleaved signal peptide that may contribute to its cytoplasmic localization. Importantly, an ~10-kDa proteinase K-resistant PrP fragment was detected, which was the same as those observed in patients suffering from this type of prion diseases. To our knowledge, this is the first animal study of familial prion disease caused by Q159X that recapitulates key features of human disease. It will be a valuable tool for investigating the pathogenic mechanisms underlying familial prion diseases caused by nonsense mutations.

Prions: structure, function, evolution, and disease

Prions are proteinaceous infectious particles implicated in fatal neurodegenerative disorders known as prion diseases. Herein, we provide an overview of prion biology, emphasizing the structural, functional, and evolutionary aspects of prions, along with their potential applications in protein engineering. Understanding the structure-function relationships of both healthy and disease-associated prion proteins enables a deeper understanding of the mechanisms of prion-induced neurotoxicity. Furthermore, we describe how insights into prion evolution have begun to shed light on their ancient origins and evolutionary resilience, offering deeper insights into the potential roles of prions in primordial chemical processes.

SARS-CoV-2 and HSV-1 Induce Amyloid Aggregation in Human CSF Resulting in Drastic Soluble Protein Depletion

The corona virus (SARS-CoV-2) pandemic and the resulting long-term neurological complications in patients, known as long COVID, have renewed interest in the correlation between viral infections and neurodegenerative brain disorders. While many viruses can reach the central nervous system (CNS) causing acute or chronic infections (such as herpes simplex virus 1, HSV-1), the lack of a clear mechanistic link between viruses and protein aggregation into amyloids, a characteristic of several neurodegenerative diseases, has rendered such a connection elusive. Recently, we showed that viruses can induce aggregation of purified amyloidogenic proteins via the direct physicochemical mechanism of heterogeneous nucleation (HEN). In the current study, we show that the incubation of HSV-1 and SARS-CoV-2 with human cerebrospinal fluid (CSF) leads to the amyloid aggregation of several proteins known to be involved in neurodegenerative diseases, such as APLP1 (amyloid β precursor like protein 1), ApoE, clusterin, α2-macroglobulin, PGK-1 (phosphoglycerate kinase 1), ceruloplasmin, nucleolin, 14-3-3, transthyretin, and vitronectin. Importantly, UV-inactivation of SARS-CoV-2 does not affect its ability to induce amyloid aggregation, as amyloid formation is dependent on viral surface catalysis via HEN and not its ability to replicate. Additionally, viral amyloid induction led to a dramatic drop in the soluble protein concentration in the CSF. Our results show that viruses can physically induce amyloid aggregation of proteins in human CSF and result in soluble protein depletion, thus providing a potential mechanism that may account for the association between persistent and latent/reactivating brain infections and neurodegenerative diseases.

Quantifying the Molecular Properties of the Elk Chronic Wasting Disease Agent with Mass Spectrometry

Chronic wasting disease (CWD) is a prion disease afflicting wild and farmed elk. CWD prions (PrPSc) are infectious protein conformations that replicate by inducing a natively expressed prion protein (PrPC) to refold into the prion conformation. Mass spectrometry was used to study the prions resulting from a previously described experimental inoculation of MM132, ML132, and LL132 elk with a common CWD inoculum. Chymotryptic digestion times and instrument parameters were optimized to yield a set of six peptides, TNMK, MLGSAMSRPL, LLGSAMSRPL, ENMYR, MMER, and VVEQMCITQYQR. These peptides were used to quantify the amount, the M132 and L132 polymorphic composition, and the extent of methionine oxidation of elk PrPSc. The amount (ng/g brain tissue) of PrPSc present in each sample was determined to be: MM132 (5.4 × 102 ± 7 × 101), ML132 (3.3 × 102 ± 6 × 101 and 3.6 × 102 ± 3 × 101) and LL132 (0.7 × 102 ± 1 × 101, 0.2 × 102 ± 0.2 × 101, and 0.2 × 102 ± 0.5 × 101). The proportion of L132 polymorphism in ML132 (heterozygous) PrPSc from CWD-infected elk was determined to be 43% ± 2% or 36% ± 3%. Methionine oxidation was detected and quantified for the M132 and L132 polymorphisms in the samples. In this way, mass spectrometry can be used to characterize prion strains at a molecular level.

Minor prion substrains overcome transmission barriers

Mammalian prion diseases are infectious neurodegenerative diseases caused by the self-templating form of the prion protein PrPSc. Much evidence supports the hypothesis that prions exist as a mixture of a dominant strain and minor prion strains. While it is known that prions can infect new species, the relative contribution of the dominant prion strain and minor strains in crossing the species barrier is unknown. We previously identified minor prion strains from a biologically cloned drowsy (DY) strain of hamster-adapted transmissible mink encephalopathy (TME). Here we show that these minor prion strains have increased infection efficiency to rabbit kidney epithelial cells that express hamster PrPC compared to the dominant strain DY TME. Using protein misfolding cyclic amplification (PMCA), we found that the dominant strain DY TME failed to convert mouse PrPC to PrPSc, even after several serial passages. In contrast, the minor prion strains isolated from biologically cloned DY TME robustly converted mouse PrPC to PrPSc in the first round of PMCA. This observation indicates that minor prion strains from the mutant spectra contribute to crossing the species barrier. Additionally, we found that the PMCA conversion efficiency for the minor prion strains tested was significantly different from each other and from the short-incubation period prion strain HY TME. This suggests that minor strain diversity may be greater than previously anticipated. These observations further expand our understanding of the mechanisms underlying the species barrier effect and has implications for assessing the zoonotic potential of prions.

IMPORTANCE

Prions from cattle with bovine spongiform encephalopathy have transmitted to humans, whereas scrapie from sheep and goats likely has not, suggesting that some prions can cross species barriers more easily than others. Prions are composed of a dominant strain and minor strains, and the contribution of each population to adapt to new replicative environments is unknown. Recently, minor prion strains were isolated from the biologically cloned prion strain DY TME, and these minor prion strains differed in properties from the dominant prion strain, DY TME. Here we found that these minor prion strains also differed in conversion efficiency and host range compared to the dominant strain DY TME. These novel findings provide evidence that minor prion strains contribute to interspecies transmission, underscoring the significance of minor strain components in important biological processes.

Protein aggregation in health and disease: A looking glass of two faces

Protein molecules organize into an intricate alphabet of twenty amino acids and five architecture levels. The jargon "one structure, one functionality" has been challenged, considering the amount of intrinsically disordered proteins in the human genome and the requirements of hierarchical hetero- and homo-protein complexes in cell signaling. The assembly of large protein structures in health and disease is now viewed through the lens of phase separation and transition phenomena. What drives protein misfolding and aggregation? Or, more fundamentally, what hinders proteins from maintaining their native conformations, pushing them toward aggregation? Here, we explore the principles of protein folding, phase separation, and aggregation, which hinge on crucial events such as the reorganization of solvents, the chemical properties of amino acids, and their interactions with the environment. We focus on the dynamic shifts between functional and dysfunctional states of proteins and the conditions that promote protein misfolding, often leading to disease. By exploring these processes, we highlight potential therapeutic avenues to manage protein aggregation and reduce its harmful impacts on health.