Differential effects of prion particle size on infectivity in vivo and in vitro

Highly infectious CJD particles lack prion protein but contain many viral-linked peptides by LC-MS/MS

It is widely believed that host prion protein (PrP), without nucleic acid, converts itself into an infectious form (PrP‐res) that causes transmissible encephalopathies (TSEs), such as human sporadic CJD (sCJD), endemic sheep scrapie, and epidemic BSE. There are many detailed investigations of PrP, but proteomic studies of other proteins in verified infectious TSE particles have not been pursued, even though brain homogenates without PrP retain their complete infectious titer. To define proteins that may be integral to, process, or protect an agent genome, we developed a streamlined, high‐yield purification of infectious FU‐CJD mouse brain particles with minimal PrP. Proteinase K (PK) abolished all residual particle PrP, but did not reduce infectivity, and viral‐size particles lacking PrP were ∼70S (vs. 90–120S without PK). Furthermore, over 1,500 non‐PrP proteins were still present and positively identified in high titer FU‐CJD particles without detectable PrP by mass spectrometry (LC‐MS/MS); 114 of these peptides were linked to viral motifs in the environmental–viral database, and not evident in parallel uninfected controls. Host components were also identified in both PK and non‐PK treated particles from FU‐CJD mouse brain and human sCJD brain. This abundant cellular data had several surprises, including finding Huntingtin in the sCJD but not normal human brain samples. Similarly, the neural Wiskott–Aldrich sequence and multivesicular and endosome components associated with retromer APP (Alzheimer amyloid) processing were only in sCJD. These cellular findings suggest that new therapies directed at retromer–vesicular trafficking in other neurodegenerative diseases may also counteract late‐onset sCJD PrP amyloid pathology. J. Cell. Biochem. 115: 2012–2021, 2014. © 2014 Wiley Periodicals, Inc.

A specific population of abnormal prion protein aggregates is preferentially taken up by cells and disaggregated in a strain-dependent manner

Prion diseases are characterized by the conversion of the soluble protease-sensitive host-encoded prion protein (PrP(C)) into its aggregated, protease-resistant, and infectious isoform (PrP(Sc)). One of the earliest events occurring in cells following exposure to an exogenous source of prions is the cellular uptake of PrP(Sc). It is unclear how the biochemical properties of PrP(Sc) influence its uptake, although aggregate size is thought to be important. Here we show that for two different strains of mouse prions, one that infects cells (22L) and one that does not (87V), a fraction of PrP(Sc) associated with distinct sedimentation properties is preferentially taken up by the cells. However, while the fraction of PrP(Sc) and the kinetics of uptake were similar for both strains, PrP(Sc) derived from the 87V strain was disaggregated more rapidly than that derived from 22L. The increased rate of PrP(Sc) disaggregation did not correlate with either the conformational or aggregate stability of 87V PrP(Sc), both of which were greater than those of 22L PrP(Sc). Our data suggest that the kinetics of disaggregation of PrP(Sc) following cellular uptake is independent of PrP(Sc) stability but may be dependent upon some component of the PrP(Sc) aggregate other than PrP. Rapid disaggregation of 87V PrP(Sc) by the cell may contribute, at least in part, to the inability of 87V to infect cells in vitro.

Establishing quantitative real-time quaking-induced conversion (qRT-QuIC) for highly sensitive detection and quantification of PrPSc in prion-infected tissues

Background

PrP^Sc, the only known constituent of prions, the infectious agents causing prion diseases, can be detected by real-time quaking-induced conversion (RT-QuIC). However, there is no efficient method to quantify the amount of PrP^Sc by RT-QuIC.

Results

Here we introduce quantitative RT-QuIC (qRT-QuIC) to quantify with high accuracy minute amounts of PrP^Sc in the brain and various peripheral tissues at levels far below detection by in vivo transmission. PrP^Sc is relatively resistant to treatment with proteinase K (PK). However, as there can also be a fraction of pathological PrP that is digested by PK, we use the term PrP^27-30 to denote to the amount of PrP^Sc that can be detected by immunoblot after PK treatment. qRT-QuIC is based upon the quantitative correlation between the seeded amount of PrP^27-30 and the lag time to the start of the conversion reaction detected by RT-QuIC. By seeding known amounts of PrP^27-30 quantified by immunoblot into qRT-QuIC a standard calibration curve can be obtained. Based on this calibration curve, seeded undetermined amounts of PrP^27-30 can be directly calculated. qRT-QuIC allowed to quantify PrP^27-30 concentrations at extremely low levels as low as 10^-15.5 g PrP^27-30, which corresponds to 0.001 LD₅₀ units obtained by in vivo i.c. transmission studies. We find that PrP^27-30 concentration increases steadily in the brain after inoculation and can be detected at various time points during the incubation period in peripheral organs (spleen, heart, muscle, liver, kidney) in two experimental scrapie strains (RML, ME7) in the mouse.

Conclusions

We suggest that an automatic quantitative system to measure disease progression as well as prion contamination of organs, blood and food product is feasible. Moreover, the concept of qRT-QuIC should be applicable to measure other disease-associated proteins rich in β-pleated structures (amyloid) that bind ThT and that show seeded aggregation.

Analyses of protease resistance and aggregation state of abnormal prion protein across the spectrum of human prions

Prion diseases are characterized by tissue accumulation of a misfolded, β-sheet-enriched isoform (scrapie prion protein (PrP(Sc))) of the cellular prion protein (PrP(C)). At variance with PrP(C), PrP(Sc) shows a partial resistance to protease digestion and forms highly aggregated and detergent-insoluble polymers, two properties that have been consistently used to distinguish the two proteins. In recent years, however, the idea that PrP(Sc) itself comprises heterogeneous species has grown. Most importantly, a putative proteinase K (PK)-sensitive form of PrP(Sc) (sPrP(Sc)) is being increasingly investigated for its possible role in prion infectivity, neurotoxicity, and strain variability. The study of sPrP(Sc), however, remains technically challenging because of the need of separating it from PrP(C) without using proteases. In this study, we have systematically analyzed both PK resistance and the aggregation state of purified PrP(Sc) across the whole spectrum of the currently characterized human prion strains. The results show that PrP(Sc) isolates manifest significant strain-specific differences in their PK digestion profile that are only partially explained by differences in the size of aggregates, suggesting that other factors, likely acting on PrP(Sc) aggregate stability, determine its resistance to proteolysis. Fully protease-sensitive low molecular weight aggregates were detected in all isolates but in a limited proportion of the overall PrP(Sc) (i.e. <10%), arguing against a significant role of slowly sedimenting PK-sensitive PrP(Sc) in the biogenesis of prion strains. Finally, we highlight the limitations of current operational definitions of sPrP(Sc) and of the quantitative analytical measurements that are not based on the isolation of a fully PK-sensitive PrP(Sc) form.

Prion subcellular fractionation reveals infectivity spectrum, with a high titre-low PrPres level disparity

BACKGROUND

Prion disease transmission and pathogenesis are linked to misfolded, typically protease resistant (PrPres) conformers of the normal cellular prion protein (PrPC), with the former posited to be the principal constituent of the infectious 'prion'. Unexplained discrepancies observed between detectable PrPres and infectivity levels exemplify the complexity in deciphering the exact biophysical nature of prions and those host cell factors, if any, which contribute to transmission efficiency. In order to improve our understanding of these important issues, this study utilized a bioassay validated cell culture model of prion infection to investigate discordance between PrPres levels and infectivity titres at a subcellular resolution.

FINDINGS

Subcellular fractions enriched in lipid rafts or endoplasmic reticulum/mitochondrial marker proteins were equally highly efficient at prion transmission, despite lipid raft fractions containing up to eight times the levels of detectable PrPres. Brain homogenate infectivity was not differentially enhanced by subcellular fraction-specific co-factors, and proteinase K pre-treatment of selected fractions modestly, but equally reduced infectivity. Only lipid raft associated infectivity was enhanced by sonication.

CONCLUSIONS

This study authenticates a subcellular disparity in PrPres and infectivity levels, and eliminates simultaneous divergence of prion strains as the explanation for this phenomenon. On balance, the results align best with the concept that transmission efficiency is influenced more by intrinsic characteristics of the infectious prion, rather than cellular microenvironment conditions or absolute PrPres levels.

PK-sensitive PrP is infectious and shares basic structural features with PK-resistant PrP

One of the main characteristics of the transmissible isoform of the prion protein (PrP^Sc) is its partial resistance to proteinase K (PK) digestion. Diagnosis of prion disease typically relies upon immunodetection of PK-digested PrP^Sc following Western blot or ELISA. More recently, researchers determined that there is a sizeable fraction of PrP^Sc that is sensitive to PK hydrolysis (sPrP^Sc). Our group has previously reported a method to isolate this fraction by centrifugation and showed that it has protein misfolding cyclic amplification (PMCA) converting activity. We compared the infectivity of the sPrP^Sc versus the PK-resistant (rPrP^Sc) fractions of PrP^Sc and analyzed the biochemical characteristics of these fractions under conditions of limited proteolysis. Our results show that sPrP^Sc and rPrP^Sc fractions have comparable degrees of infectivity and that although they contain different sized multimers, these multimers share similar structural properties. Furthermore, the PK-sensitive fractions of two hamster strains, 263K and Drowsy (Dy), showed strain-dependent differences in the ratios of the sPrP^Sc to the rPrP^Sc forms of PrP^Sc. Although the sPrP^Sc and rPrP^Sc fractions have different resistance to PK-digestion, and have previously been shown to sediment differently, and have a different distribution of multimers, they share a common structure and phenotype.

Prion diseases are protein misfolding disorders. Different strains of prions are known to have variable resistance to proteinase K (PK) digestion. Furthermore, the same strain possesses both a PK sensitive (sPrP^Sc) and PK resistant (rPrP^Sc) aggregate of PrP. We developed methods to isolate the sPrP^Sc from rPrP^Sc fraction of the 263K strain of hamster-adapted scrapie. Both fractions were infectious, but have different physico-chemical properties. When we analyzed the lesion targets in the brain produced by each fraction they were essentially identical, suggesting that they were the same strain. The biochemical differences in the phenotypes of these two fractions are due to different sized multimers that share common structural properties. Furthermore, the comparison of the sensitive fractions of two hamster strains, 263K and Drowsy (Dy), showed strain-dependent differences in the ratios of the PK-sensitive to the PK-resistant forms of PrP^Sc.

Lower specific infectivity of protease-resistant prion protein generated in cell-free reactions

Prions are unconventional infectious agents that cause transmissible spongiform encephalopathy (TSE) diseases, or prion diseases. The biochemical nature of the prion infectious agent remains unclear. Previously, using a protein misfolding cyclic amplification (PMCA) reaction, infectivity and disease-associated protease-resistant prion protein (PrPres) were both generated under cell-free conditions, which supported a nonviral hypothesis for the agent. However, these studies lacked comparative quantitation of both infectivity titers and PrPres, which is important both for biological comparison with in vivo-derived infectivity and for excluding contamination to explain the results. Here during four to eight rounds of PMCA, end-point dilution titrations detected a >320-fold increase in infectivity versus that in controls. These results provide strong support for the hypothesis that the agent of prion infectivity is not a virus. PMCA-generated samples caused the same clinical disease and neuropathology with the same rapid incubation period as the input brain-derived scrapie samples, providing no evidence for generation of a new strain in PMCA. However, the ratio of the infectivity titer to the amount of PrPres (specific infectivity) was much lower in PMCA versus brain-derived samples, suggesting the possibility that a substantial portion of PrPres generated in PMCA might be noninfectious.

Prion seeded conversion and amplification assays

The conversion of the normal prion protein (PrP(C)) into its misfolded, aggregation-prone and infectious (prion) isoform is central to the progression of transmissible spongiform encephalopathies (TSEs) or prion diseases. Since the initial development of a cell free PrP conversion reaction, striking progress has been made in the development of much more continuous prion-induced conversion and amplification reactions. These studies have provided major insights into the molecular underpinnings of prion propagation and enabled the development of ultra-sensitive tests for prions and prion disease diagnosis. This chapter will provide an overview of such reactions and the practical and fundamental consequences of their development.

Prion dynamics with size dependency-strain phenomena

Models for the polymerization process involved in prion self-replication are well-established and studied [H. Engler, J. Pruss, and G.F. Webb, Analysis of a model for the dynamics of prions II, J. Math. Anal. Appl. 324 (2006), pp. 98-117; M.L. Greer, L. Pujo-Menjouet, and G.F. Webb, A mathematical analysis of the dynamics of prion proliferation, J. Theoret. Biol. 242 (2006), pp. 598-606; J. Pruss, L. Pujo-Menjouet, G.F. Webb, and R. Zacher, Analysis of a model for the dynamics of prions, Discrete Cont. Dyn. Sys. Ser. B 6(1) (2006), pp. 215-225] in the case where the dynamics coefficients do not depend on the size of polymers. However, several experimental studies indicate that the structure and size of the prion aggregates are determinant for their pathological effect. This motivated the analysis in Calvez et al. [Size distribution dependence of prion aggregates infectivity, Math Biosci. 217 (2009), pp. 88-99] where the authors take into account size-dependent replicative properties of prion aggregates. We first improve a result concerning the dynamics of prion aggregates when a pathological state exists (high production of the normal protein). Then we study the strain phenomena and more specifically we wonder what specific replicative properties are determinant in strain propagation. We propose to interpret it also as a dynamical property of size repartitions.

Hyperefficient PrP Sc amplification of mouse-adapted BSE and scrapie strain by protein misfolding cyclic amplification technique

Abnormal forms of prion protein (PrP(Sc)) accumulate via structural conversion of normal PrP (PrP(C)) in the progression of transmissible spongiform encephalopathy. Under cell-free conditions, the process can be efficiently replicated using in vitro PrP(Sc) amplification methods, including protein misfolding cyclic amplification. These methods enable ultrasensitive detection of PrP(Sc); however, there remain difficulties in utilizing them in practice. For example, to date, several rounds of protein misfolding cyclic amplification have been necessary to reach maximal sensitivity, which not only take several weeks, but also result in an increased risk of contamination. In this study, we sought to further promote the rate of PrP(Sc) amplification in the protein misfolding cyclic amplification technique using mouse transmissible spongiform encephalopathy models infected with either mouse-adapted bovine spongiform encephalopathy or mouse-adapted scrapie, Chandler strain. Here, we demonstrate that appropriate regulation of sonication dramatically accelerates PrP(Sc) amplification in both strains. In fact, we reached maximum sensitivity, allowing the ultrasensitive detection of < 1 LD(50) of PrP(Sc) in the diluted brain homogenates, after only one or two reaction rounds, and in addition, we detected PrP(Sc) in the plasma of mouse-adapted bovine spongiform encephalopathy-infected mice. We believe that these results will advance the establishment of a fast, ultrasensitive diagnostic test for transmissible spongiform encephalopathies.