Implications of gut microbiota dysbiosis and metabolic changes in prion disease.

Evidence of the gut microbiota influencing neurodegenerative diseases has been reported for several neural diseases. However, there is little insight regarding the relationship between the gut microbiota and prion disease. Here, using fecal samples of 12 prion-infected mice and 25 healthy controls, we analyzed the structure of the gut microbiota and metabolic changes by 16S rRNA sequencing and LC-MS-based metabolomics respectively as multi-omic analyses. Additionally, SCFAs and common amino acids were detected by GC-MS and UPLC respectively. Enteric changes induced by prion disease affected both structure and abundances of the gut microbiota. The gut microbiota of infected mice displayed greater numbers of Proteobacteria and less Saccharibacteria at the phylum level and more Lactobacillaceae and Helicobacteraceae and less Prevotellaceae and Ruminococcaceae at the family level. A total of 145 fecal metabolites were found to be significantly different in prion infection, and most (114) of these were lipid metabolites. Using KEGG pathway enrichment analysis, we found that 3 phosphatidylcholine (PC) compounds significantly decreased and 4 hydrophobic bile acids significantly increased. Decreases of 8 types of short-chain acids (SCFAs) and increases of Cys and Tyr and decreases of His, Trp, and Arg were observed in prion infection. Correlation analysis indicated that the gut microbiota changes observed in our study may have been the shared outcome of prion disease. These findings suggest that prion disease can cause significant shifts in the gut microbiota. Certain bacterial taxa can then respond to the resulting change to the enteric environment by causing dramatic shifts in metabolite levels. Our data highlight the health impact of the gut microbiota and related metabolites in prion disease.

Novel Spiroplasma sp. Isolated From CWD Is an Extreme Bacterial Thermoacidophile That Survives Autoclaving, Boiling, Formalin Treatment, and Significant Gamma Irradiation.

Rapid spreading of chronic wasting disease (CWD) in wildlife and captive cervid populations has exposed lack of progress in dealing with the transmissible spongiform encephalopathies (TSE) of man and animals. Since the TSE transmissible agent was resistant to extremes in environmental and chemical treatments, focus was on an unconventional agent including the prion theory. Recent breakthrough research has revealed consistent isolation of a novel Spiroplasma sp. from TSE-affected tissues that propagates in cell-free media and on agar. Here, we developed a live culture assay to test whether the CWD spiroplasma isolate possessed unconventional biologic properties akin to those of the transmissible agent of TSE. The CWD spiroplasma isolate survived boiling for 1 hour, standard liquid autoclaving, 10% formalin treatment overnight, and gamma irradiation of 20 kGy. The CWD spiroplasma isolate is an acidophile, growing best at pH 2. The biologic resistance of the CWD spiroplasma isolate may be due to unusual phage-like viruses found in the bacterial pellet or to DNA-protein binding. Because the CWD spiroplasma isolate has biologic properties consistent with the causal agent of the TSEs, TSE research focus should be redirected to development of diagnostic tests and preventive vaccines for control of CWD based upon the bacterium.

Amplification techniques and diagnosis of prion diseases.

Protein misfolding cyclic amplification assay (PMCA) and real-time quaking-induced conversion (RT-QuIC) are two amplification techniques based on the ability of PrPsc to induce a conformational change in PrP allowing the detection of minute amounts of PrPsc in body fluids or tissues. PMCA and RT-QuIC have different ability to amplify PrPsc from sporadic, variant and genetic forms of Creutzfeldt-Jakob disease (CJD). PMCA readily amplifies PrPsc from variant CJD (vCJD) tissue while RT-QuIC easily amplifies PrPsc from sporadic CJD (sCJD) patient tissues. In terms of diagnosis, this implies the possibility of distinguishing vCJD from sCJD and explains the wider use of RT-QuIC given the respective frequencies of vCJD and sCJD. The sensitivity values of RT-QuIC for the diagnosis of sCJD are comparable or higher than those of the other tests (EEG, MRI, detection of 14-3-3 or tau proteins in cerebrospinal fluid) but with a specificity close to 100%. These new diagnostic methods could also be useful for the diagnosis of other neurodegenerative diseases.

Novel Spiroplasma Spp. Cultured From Brains and Lymph Nodes From Ruminants Affected With Transmissible Spongiform Encephalopathy.

Spiroplasma spp., tiny filterable wall-less bacteria, are consistently associated with the transmissible spongiform encephalopathies (TSE). Spiral forms have been transiently isolated from TSE-affected brain tissues in SP4 growth media designed for isolation of Spiroplasma spp., but the isolate could not be propagated in SP4 media. A bacterium must grow in vitro in cell-free cultures to allow full characterization of a suspect pathogen. Here, a novel Spiroplasma sp. was isolated from scrapie- and chronic wasting disease (CWD)-affected brains and lymph nodes. Filtrates of tissue homogenates inoculated into Brucella media incubated for 14 days at 35 °C resulted in high titers of spiroplasma as shown by dark-field microscopy. A drop assay of infected media on Bacto Schaedler agar showed spiroplasma isolates forming unique subsurface colonies after 21 days incubation. Spiroplasma coils, coccoid forms and clumps of entwined spiroplasma filaments were seen on the agar by scanning electron microscopy. Since Brucella media has a sodium bisulfite additive that lowers oxygen tension, TSE spiroplasma growth requires media with low oxygen tension. Brucella media allows for isolation and propagation of spiroplasma from TSE-affected tissues, which will lead to complete characterization of this TSE pathogen and determine its role as a candidate causative agent of TSE.

Diversity of Gut Microbiota Metabolic Pathways in 10 Pairs of Chinese Infant Twins.

Early colonization of gut microbiota in human gut is a complex process. It remains unclear when gut microbiota colonization occurs and how it proceeds. In order to study gut microbiota composition in human early life, the present study recruited 10 healthy pairs of twins, including five monozygotic (MZ) and five dizygotic (DZ) twin pairs, whose age ranged from 0 to 6 years old. 20 fecal samples from these twins were processed by shotgun metagenomic sequencing, and their averaged data outputs were generated as 2G per sample. We used MEGAN5 to perform taxonomic and functional annotation of the metagenomic data, and systematically analyzed those 20 samples, including Jaccard index similarity, principle component, clustering, and correlation analyses. Our findings indicated that within our study group: 1) MZ-twins share more microbes than DZ twins or non-twin pairs, 2) gut microbiota distribution is relatively stable at metabolic pathways level, 3) age represents the strongest factor that can account for variation in gut microbiota, and 4) a clear metabolic pathway shift can be observed, which speculatively occurs around the age of 1 year old. This research will serve as a base for future studies of gut microbiota-related disease research.

Spiroplasma spp. biofilm formation is instrumental for their role in the pathogenesis of plant, insect and animal diseases.

Spiroplasma spp. are important phyto and insect pathogens, and candidate causal agent/s of transmissible spongiform encephalopathies (TSE) in man and animals. These filterable wall-less bacteria are widely distributed in nature with an unspecified environmental reservoir. In this study we showed by scanning electron microscopy that spiroplasma form biofilm on an assortment of hard surfaces including mica, nickel and stainless steel. Spiroplasma were stuck to the surfaces by fibrillar threads consistent with curli fibers (an amyloid protein found in bacterial biofilms). After a lengthy time in cultures (6 weeks), spiroplasma in biofilm bound to mica disks lost their spiral shapes and formed coccoid forms interconnected by long (>2 µm) branched membranous nanotubules, therein representing direct conjugate connections between the cells. The affinity of spiroplasma biofilms for mica and nickel, and the membrane communications suggest that soil could be a reservoir for these bacteria. The persistence of clay bound spiroplasma in soil could serve as the mechanism of lateral spread of TSEs by ingestion of soil by ruminants. Spiroplasma binding to stainless steel wire supports bacterial contamination of surgical instruments following surgery on dementia patients as a mechanism of iatrogenic transmission of TSEs, especially with resistance of spiroplasma in biofilms to drying or exposure to 50% glutaraldehyde. The discovery of biofilm formation by spiroplasma addresses questions regarding environmental persistence of these organisms in nature and suggests novel mechanisms of intercellular communication and transmission.

Amyloid of the Candida albicans Ure2p prion domain is infectious and has an in-register parallel ß-sheet structure.

Ure2p of Candida albicans (Ure2(albicans) or CaUre2p) can be a prion in Saccharomyces cerevisiae, but Ure2p of Candida glabrata (Ure2(glabrata)) cannot, even though the Ure2(glabrata) N-terminal domain is more similar to that of the S. cerevisiae Ure2p (Ure2(cerevisiae)) than Ure2(albicans) is. We show that the N-terminal N/Q-rich prion domain of Ure2(albicans) forms amyloid that is infectious, transmitting [URE3alb] to S. cerevisiae cells expressing only C. albicans Ure2p. Using solid-state nuclear magnetic resonance of selectively labeled C. albicans Ure2p(1-90), we show that this infectious amyloid has an in-register parallel ß-sheet structure, like that of the S. cerevisiae Ure2p prion domain and other S. cerevisiae prion amyloids. In contrast, the N/Q-rich N-terminal domain of Ure2(glabrata) does not readily form amyloid, and that formed upon prolonged incubation is not infectious.

Survival of infectious prions in water.

The objective of this study was to evaluate the fate of infectious prions in water. Known concentrations of infectious prions were added to deionized water, tap water, and wastewater. Samples were incubated at 25°C, 37°C, and 50°C for 1 to 8 weeks. The standard scrapie cell assay (SSCA) which includes the ELISPOT (Enzyme Linked Immuno-Spot) reaction was performed to determine prion infectivity and quantity as a function of time. A reduction of infectious prions was observed at 25°C, 37°C, and 50°C ranging between 0.5-log10 and 1.4-log10 in one week. Results suggest that organic matter was instrumental in protecting infectious prions, allowing them to remain infectious for a longer period of time. Thus, our data effectively show a quantifiable reduction of infectious prions in water and identifies some of the components that may influence infectivity.

Experimental inoculation of raccoons (Procyon lotor) with Spiroplasma mirum and transmissible mink encephalopathy (TME).

The primary objective of this study was to determine whether or not Spiroplasma mirum would be capable of producing lesions of transmissible spongiform encephalopathy (TSE) when inoculated in raccoons (Procyon lotor) and, if that was possible, to compare the clinicopathological findings with those of transmissible mink encephalopathy (TME) in the same experimental model. For this purpose, 5 groups (n = 5) of raccoon kits were inoculated intracerebrally with either S. mirum and/or TME. Two other groups (n = 5) of raccoon kits served as sham-inoculated controls. All animals inoculated with TME, either alone or in combination, showed clinical signs of neurologic disorder and were euthanized within 6 mo post-inoculation (MPI). None of the carcasses revealed gross lesions. Spongiform encephalopathy was observed by light microscopy and the presence of abnormal disease-causing prion protein (PrP(d)) was detected by immunohistochemistry (IHC) and Western blot (WB) techniques in only the raccoons administered TME. Raccoons inoculated with Spiroplasma, but not administered TME agent, were euthanized at 30 MPI. They did not show clinical neurologic signs, their brains did not have lesions of spongiform encephalopathy, and their tissues were negative for S. mirum by polymerase chain reaction (PCR) and for PrP(d) by IHC and WB techniques. The results of this study indicate that Spiroplasma mirum does not induce TSE-like disease in raccoons.

Inverse correlation of thermal lability and conversion efficiency for five prion protein polymorphic variants.

Transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of deposits of an abnormal form, PrP(Sc), of the host-encoded prion protein, PrP(C). Amino acid substitutions in PrP(C) have long been known to affect TSE disease outcome. In extreme cases in humans, various mutations appear to cause disease. In animals, polymorphisms are associated with variations in disease susceptibility and, in sheep, several polymorphisms have been identified that are known to affect susceptibility of carriers to disease. The mechanisms of polymorphism-mediated modulation of disease susceptibility remain elusive, and we have been studying the effect of various amino acid substitutions at PrP codon 164 (mouse numbering), in the beta2-alpha2 loop region of the prion protein, to attempt to decipher how polymorphisms may affect disease susceptibility. Combined in vitro approaches suggest that there exists a correlation between the ability of protein variants to convert to abnormal isoforms in seeded conversion assays versus the thermal stability of the protein variants, as judged by both thermal denaturation and an unseeded in vitro oligomerization assay. We have performed molecular dynamics simulations to give an indication of backbone conformational changes as a result of amino acid changes and found that alteration of a single residue in PrP can result in local changes in structure that may affect global conformation and stability. Our results are consistent with modulation of disease susceptibility through differential protein stability leading to enhanced generic misfolding of TSE resistance-associated protein variants.

In silico comparative analysis of DNA and amino acid sequences for prion protein gene.

Genetic variability might contribute to species specificity of prion diseases in various organisms. In this study, structures of the prion protein gene (PRNP) and its amino acids were compared among species of which sequence data were available. Comparisons of PRNP DNA sequences among 12 species including human, chimpanzee, monkey, bovine, ovine, dog, mouse, rat, wallaby, opossum, chicken and zebrafish allowed us to identify candidate regulatory regions in intron 1 and 3'-untranslated region (UTR) in addition to the coding region. Highly conserved putative binding sites for transcription factors, such as heat shock factor 2 (HSF2) and myocite enhancer factor 2 (MEF2), were discovered in the intron 1. In 3'-UTR, the functional sequence (ATTAAA) for nucleus-specific polyadenylation was found in all the analysed species. The functional sequence (TTTTTAT) for maturation-specific polyadenylation was identically observed only in ovine, and one or two nucleotide mismatches in the other species. A comparison of the amino acid sequences in 53 species revealed a large sequence identity. Especially the octapeptide repeat region was observed in all the species but frog and zebrafish. Functional changes and susceptibility to prion diseases with various isoforms of prion protein could be caused by numeric variability and conformational changes discovered in the repeat sequences.

Spiroplasma spp. from transmissible spongiform encephalopathy brains or ticks induce spongiform encephalopathy in ruminants.

Spiroplasma, small motile wall-less bacteria, are linked by molecular and serological studies to the transmissible spongiform encephalopathies (TSEs), which include scrapie in sheep, chronic wasting disease (CWD) in deer and Creutzfeldt-Jakob disease in humans. In this study, two experiments were undertaken to determine the role of spiroplasma in the pathogenesis of TSE. In experiment 1, Spiroplasma mirum, a rabbit tick isolate that had previously been shown to experimentally induce spongiform encephalopathy in rodents, was inoculated intracranially (IC) into ruminants. S. mirum-inoculated deer manifested clinical signs of TSE after 1.5 to 5.5 months incubation. The deer, as well as sheep and goats, inoculated with S. mirum developed spongiform encephalopathy in a dose-dependent manner. In experiment 2, spiroplasma closely related to S. mirum were isolated from TSE-affected brains via passage in embryonated eggs, and propagated in cell-free M1D media. Spiroplasma spp. isolates from scrapie-affected sheep brain and from CWD-affected deer brain inoculated IC into sheep and goats induced spongiform encephalopathy closely resembling natural TSE in these animals. These data show spiroplasma to be consistently associated with TSE, and able experimentally to cause TSE in ruminant animal models, therein questioning the validity of studies that have concluded the prion, a miss-folded protease-resistant protein that builds up in TSE brains during the course of the disease, to be the sole causal agent. The spiroplasma infection models reported here will be important for investigating factors involved in the pathogenesis of TSE since ruminants are the natural hosts.

From rabies to transmissible spongiform encephalopathies: an immune-mediated microbial trigger involving molecular mimicry could be the answer.

The concept of experimental allergic encephalomyelitis (EAE) being linked to both rabies post-vaccination encephalomyelitis and multiple sclerosis (MS) has raised the intriguing question whether animal studies carried out for the induction and transmission of transmissible spongiform encephalopathies (TSEs) using brain antigens including prions do have a similar immunopathogenetic mechanism. Although an essential link between autoimmunity and MS has been well established, its role in the pathogenesis of TSEs is generally lacking. However, auto-antibodies to myelin proteins and/or other neuronal antigens such as neurofilaments and prion proteins have been reported in animals with bovine spongiform encephalopathy (BSE) and scrapie as well as in patients with Creutzfeld-Jakob disease (CJD) and kuru. Acinetobacter has been suggested as a possible triggering microbial factor in the initiation of the autoimmune responses in these diseases because bacterial molecular sequences resemble brain antigens, especially in animals affected with BSE and patients with MS and CJD. These possibilities need to be evaluated further with longitudinal prospective studies carried out on larger numbers of animals or humans with such diseases. The transplantation of saline suspensions of brain homogenates will evoke immunological responses and therefore, the results in the study of MS and other neurological diseases have to be interpreted with caution.

A novel copper-hydrogen peroxide formulation for prion decontamination.

With the appearance of variant Creutzfeldt-Jakob disease (CJD) and the detection of infectious prions in the peripheral organs of persons with sporadic CJD, the development of decontamination methods that are compatible with medical equipment has become a major issue. Here, we show that a formulation of copper metal ions in combination with hydrogen peroxide dramatically reduces the level of prion protein (PrP)(Sc) (the scrapie isoform of PrP) present in homogenates of samples from prion-infected brains, including brain samples from humans with CJD. An animal bioassay confirmed the reduction in prion infectivity, indicating that this novel Cu(2+)-H(2)O(2) formulation has great potential for prion decontamination.

Spiroplasma as a candidate agent for the transmissible spongiform encephalopathies.

The recovery of a novel Spiroplasma sp. from brain tissues from sheep with scrapie, cervids with chronic wasting disease, and from patients with Creutzfeldt-Jakob disease through passage through embryonated eggs has raised the issue of the role of Spiroplasma in the transmissible spongiform encephalopathies (TSE). In this review, we have inserted into an epidemiologic infection model evidence accumulated over the past 30 years showing involvement of Spiroplasma infection in TSE. These data support our hypothesis that a Spiroplasma sp. is the causal agent of TSE, although Koch's postulates must be fulfilled to definitively answer that question.

Skin-derived dendritic cells acquire and degrade the scrapie agent following in vitro exposure.

The accumulation of the scrapie agent in lymphoid tissues following inoculation via the skin is critical for efficient neuroinvasion, but how the agent is initially transported from the skin to the draining lymph node is not known. Langerhans cells (LCs) are specialized antigen-presenting cells that continually sample their microenvironment within the epidermis and transport captured antigens to draining lymph nodes. We considered LCs probable candidates to acquire and transport the scrapie agent after inoculation via the skin. XS106 cells are dendritic cells (DCs) isolated from mouse epidermis with characteristics of mature LC cells. To investigate the potential interaction of LCs with the scrapie agent XS106 cells were exposed to the scrapie agent in vitro. We show that XS106 cells rapidly acquire the scrapie agent following in vitro exposure. In addition, XS106 cells partially degrade the scrapie agent following extended cultivation. These data suggest that LCs might acquire and degrade the scrapie agent after inoculation via the skin, but data from additional experiments demonstrate that this ability could be lost in the presence of lipopolysaccharide or other immunostimulatory molecules. Our studies also imply that LCs would not undergo maturation following uptake of the scrapie agent in the skin, as the expression of surface antigens associated with LC maturation were unaltered following exposure. In conclusion, although LCs or DCs have the potential to acquire the scrapie agent within the epidermis our data suggest it is unlikely that they become activated and stimulated to transport the agent to the draining lymph node.

Novel methods for disinfection of prion-contaminated medical devices.

BACKGROUND: The unique resistance of prions to classic methods of decontamination, and evidence that prion diseases can be transmitted iatrogenically by medical devices pose a serious infection control challenge to health-care facilities. In view of the widespread tissue distribution of the variant Creutzfeldt-Jakob disease agent in human beings, new practicable decontamination procedures are urgently needed. METHODS: We adapted an in-vivo method using stainless steel wires contaminated with prions to the hamster-adapted scrapie strain 263K. A new in-vitro protocol of surface contamination compatible with subsequent biochemical detection of PrP(res) (protease-resistant form of the prion protein) from the treated surface was developed to explore the mechanisms of action of methods of decontamination under test. These models were used to investigate the effectiveness of innovative physical and chemical methods of prion inactivation. FINDINGS: Standard chemical decontamination methods (NaOH 1N, NaOCl 20000 ppm) and autoclaving in water at 134 degrees C reduced infectivity by >5.6 log10 lethal doses; autoclaving without immersion was somewhat less effective (4-4.5 log reduction). Three milder treatments, including a phenolic disinfectant, an alkaline cleaner, and the combination of an enzymatic cleaner and vaporised hydrogen peroxide (VHP) were also effective. VHP alone, which can be compatible with electronic components, achieved an approximately 4.5 log reduction in infectivity (equivalent to autoclaving without water immersion). INTERPRETATION: New decontamination procedures are proposed to ensure the safety of medical and surgical instruments as well as surfaces that cannot withstand the currently recommended prion inactivation procedures.

Glycosylation of prion strains in transmissible spongiform encephalopathies.

This is a review of prion replication in the context of the cell biology of membrane proteins especially folding quality control in the endoplasmic reticulum (ER). Transmissible spongiform encephalopathies, such as scrapie and BSE, are infectious lethal diseases of mammalian neurons characterised by conversion of the normal membrane protein PrPC to the disease-associated conformational isomer called PrPSc. PrPSc, apparently responsible for infectivity, forms a number of different conformations and specific N-glycosylation site occupancies that correlate with TSE strain differences. Dimerisation and specific binding of PrPc and PrPSc seems critical in PrPSc biosynthesis and is influenced by N-glycosylation and disulfide bond formation. PrPsc can be amplified in vitro but new glycosylation cannot occur in cell free environments without the special conditions of microsome mediated in vitro translation, thus strain specific glycosylation of PrPSc formed in vitro in the absence of these conditions must take place by imprintation of PrPc from existing glycosylation site-occupancies. PrPSc formed in cell free homogenates is not infectious pointing to events necessary for infectivity that only occur in intact cells. Such events may include glycosylation site occupancy and ER folding chaperone activity. In the biosynthetic pathway of PrPSc, early acquisition of sensitivity of the GPI anchor to phospholipase C can be distinguished from the later acquisition of protease resistance and detergent insolubility. By analogy to the co-translational formation of the MHC I loading complex, it is postulated that PrPSc or its specific peptides could imprint nascent PrPc chains thereby ensuring its own folds and the observed glycosylation site occupancy ratios of strains.