Anchorless 23-230 PrPC interactomics for elucidation of PrPC protective role

Cytoskeletal Alteration Is an Early Cellular Response in Pulmonary Epithelium Infected with Aspergillus fumigatus Rather than Scedosporium apiospermum

Invasive aspergillosis and scedosporiosis are life-threatening fungal infections with similar clinical manifestations in immunocompromised patients. Contrarily, Scedosporium apiospermum is susceptible to some azole derivative but often resistant to amphotericin B. Histopathological examination alone cannot diagnose these two fungal species. Pathogenesis studies could contribute to explore candidate protein markers for new diagnosis and treatment methods leading to a decrease in mortality. In the present study, proteomics was conducted to identify significantly altered proteins in A549 cells infected with or without Aspergillus fumigatus and S. apiospermum as measured at initial invasion. Protein validation was performed with immunogold labelling alongside immunohistochemical techniques in infected A549 cells and lungs from murine models. Further, cytokine production was measured, using the Bio-Plex-Multiplex immunoassay. The cytoskeletal proteins HSPA9, PA2G4, VAT1, PSMA2, PEX1, PTGES3, KRT1, KRT9, CLIP1 and CLEC20A were mainly changed during A. fumigatus infection, while the immunologically activated proteins WNT7A, GAPDH and ANXA2 were principally altered during S. apiospermum infection. These proteins are involved in fungal internalisation and structural destruction leading to pulmonary disorders. Interleukin (IL)-21, IL-1α, IL-22, IL-2, IL-8, IL-12, IL-17A, interferon-γ and tumour necrosis factor-α were upregulated in both aspergillosis and scedosporiosis, although more predominately in the latter, in accordance with chitin synthase-1 and matrix metalloproteinase levels. Our results demonstrated that during invasion, A. fumigatus primarily altered host cellular integrity, whereas S. apiospermum chiefly induced and extensively modulated host immune responses.

The Cellular Prion Protein and the Hallmarks of Cancer

Simple Summary

The cellular prion protein PrP^C is best known for its involvement, under its pathogenic isoform, in a group of neurodegenerative diseases. Notwithstanding, an emerging role for PrP^C in various cancer-associated processes has attracted increasing attention over recent years. PrP^C is overexpressed in diverse types of solid cancers and has been incriminated in various aspects of cancer biology, most notably proliferation, migration, invasion and metastasis, as well as resistance to cytotoxic agents. This article aims to provide a comprehensive overview of the current knowledge of PrP^C with respect to the hallmarks of cancer, a reference framework encompassing the major characteristics of cancer cells.

Abstract

Beyond its causal involvement in a group of neurodegenerative diseases known as Transmissible Spongiform Encephalopathies, the cellular prion protein PrP^C is now taking centre stage as an important contributor to cancer progression in various types of solid tumours. The prion cancer research field has progressively expanded in the last few years and has yielded consistent evidence for an involvement of PrP^C in cancer cell proliferation, migration and invasion, therapeutic resistance and cancer stem cell properties. Most recent data have uncovered new facets of the biology of PrP^C in cancer, ranging from its control on enzymes involved in immune tolerance to its radio-protective activity, by way of promoting angiogenesis. In the present review, we aim to summarise the body of literature dedicated to the study of PrP^C in relation to cancer from the perspective of the hallmarks of cancer, the reference framework defined by Hanahan and Weinberg.

Prion protein oligomers cause neuronal cytoskeletal damage in rapidly progressive Alzheimer's disease

Background

High-density oligomers of the prion protein (HDPs) have previously been identified in brain tissues of patients with rapidly progressive Alzheimer’s disease (rpAD). The current investigation aims at identifying interacting partners of HDPs in the rpAD brains to unravel the pathological involvement of HDPs in the rapid progression.

Methods

HDPs from the frontal cortex tissues of rpAD brains were isolated using sucrose density gradient centrifugation. Proteins interacting with HDPs were identified by co-immunoprecipitation coupled with mass spectrometry. Further verifications were carried out using proteomic tools, immunoblotting, and confocal laser scanning microscopy.

Results

We identified rpAD-specific HDP-interactors, including the growth arrest specific 2-like 2 protein (G2L2). Intriguingly, rpAD-specific disturbances were found in the localization of G2L2 and its associated proteins i.e., the end binding protein 1, α-tubulin, and β-actin.

Discussion

The results show the involvement of HDPs in the destabilization of the neuronal actin/tubulin infrastructure. We consider this disturbance to be a contributing factor for the rapid progression in rpAD.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13024-021-00422-x.

Effects of PrPC on DF-1 cells' biological processes and RNA-seq-based analysis of differential genes

To reveal the effects of PrP^C on cells' biological processes and on gene expression. We established stable DF-1 (PrP^C -knockdown (KD)) cells, and combined with DF-1 (wt) and DF-1 (PrP^C -overexpression (OE)) cells that we previously established we studied the effects of chicken PrP^C (PrP^C ) on DF-1 cells' processes. Then by using high throughput sequencing technology (HTS) and bioinformatics, we analyzed the differentially expressed genes (DEGs) between these cells. The results show that compared with DF-1 (wt) and DF-1 (PrP^C -scramble), DF-1 (PrP^C -KD) are significantly decreased in adhesion, proliferation, formation rate of colony and cells number of colony, scratch wound healing rate, cells number of invasion and migration, S phase cell populations, but the apoptosis rate and G1 phase cell populations are significantly increased. Conversely, all of these features in DF-1 (PrP^C -OE) are opposite. In addition, compared with DF-1 (wt), we found that there are totally 1055 DE genes between DF-1 (PrP^C -KD) and DF-1 (PrP^C -OE) cells. After Go and pathway enrichment analysis, we know that these DEGs are significantly enriched in cell, cell part, cellular process, and metabolic pathway. In short, we found that PrP^C can promote DF-1 cells' processes except apoptosis. Furthermore, PrP^C involves in the focal adhesion, cancer, ribosome, metabolic pathways, and so forth, and the overexpression of PrP^C can promote the pathway of amoebiasis, but its down-regulation can promote the pathway of serotonergic synapse. However, the details are keeping unknown and that would be our next research.

Prion Protein Interactome: Identifying Novel Targets in Slowly and Rapidly Progressive Forms of Alzheimer's Disease

Rapidly progressive Alzheimer's disease (rpAD) is a variant of AD distinguished by a rapid decline in cognition and short disease duration from onset to death. While attempts to identify rpAD based on biomarker profile classifications have been initiated, the mechanisms which contribute to the rapid decline and prion mimicking heterogeneity in clinical signs are still largely unknown. In this study, we characterized prion protein (PrP) expression, localization, and interactome in rpAD, slow progressive AD, and in non-dementia controls. PrP along with its interacting proteins were affinity purified with magnetic Dynabeads Protein-G, and were identified using Q-TOF-ESI/MS analysis. Our data demonstrated a significant 1.2-fold decrease in di-glycosylated PrP isoforms specifically in rpAD patients. Fifteen proteins appeared to interact with PrP and only two proteins3/4histone H2B-type1-B and zinc alpha-2 protein3/4were specifically bound with PrP isoform isolated from rpAD cases. Our data suggest distinct PrP involvement in association with the altered PrP interacting protein in rpAD, though the pathophysiological significance of these interactions remains to be established.

Cytoskeleton-Associated Risk Modifiers Involved in Early and Rapid Progression of Sporadic Creutzfeldt-Jakob Disease

A high priority in the prion field is to identify pre-symptomatic events and associated profile of molecular changes. In this study, we demonstrate the pre-symptomatic dysregulation of cytoskeleton assembly and its associated cofilin-1 pathway in strain and brain region-specific manners in MM1 and VV2 subtype-specific Creutzfeldt-Jakob disease at clinical and pre-clinical stage. At physiological level, PrP^C interaction with cofilin-1 and phosphorylated form of cofilin (p-cofilin(Ser3)) was investigated in primary cultures of mouse cortex neurons (PCNs) of PrP^C wild-type and knockout mice (PrP^-/-). Short-interfering RNA downregulation of active form of cofilin-1 resulted in the redistribution/downregulation of PrP^C, increase of activated form of microglia, accumulation of dense form of F-actin, and upregulation of p-cofilin(Ser3). This upregulated p-cofilin(Ser3) showed redistribution of expression predominantly in the activated form of microglia in PCNs. At pathological level, cofilin-1 expression was significantly altered in cortex and cerebellum in both humans and mice at pre-clinical stage and at early symptomatic clinical stage of the disease. Further, to better understand the possible mechanism of dysregulation of cofilin-1, we also demonstrated alterations in upstream regulators; LIM kinase isoform 1 (LIMK1), slingshot phosphatase isoform 1 (SSH1), RhoA-associated kinase (Rock2), and amyloid precursor protein (APP) in sporadic Creutzfeldt-Jakob disease MM1 mice and in human MM1 and VV2 frontal cortex and cerebellum samples. In conclusion, our findings demonstrated for the first time a key pre-clinical response of cofilin-1 and the associated pathway in prion disease.

Molecular Alterations in the Cerebellum of Sporadic Creutzfeldt-Jakob Disease Subtypes with DJ-1 as a Key Regulator of Oxidative Stress

Cerebellar damage and granular and Purkinje cell loss in sporadic Creutzfeldt-Jakob disease (sCJD) highlight a critical involvement of the cerebellum during symptomatic progression of the disease. In this project, global proteomic alterations in the cerebellum of brain from the two most prevalent subtypes (MM1 and VV2) of sCJD were studied. Two-dimensional gel electrophoresis (2DE) coupled mass spectrometric identification revealed 40 proteins in MM1 and 43 proteins in VV2 subtype to be differentially expressed. Of those, 12 proteins showed common differential expression in their expression between two subtypes. Differentially expressed proteins mainly belonged to (i) cell cycle, gene expression and cell death; (ii) cellular stress response/oxidative stress (OS) and (iii) signal transduction and synaptic functions, related molecular functions. We verified 10 differentially expressed proteins at transcriptional and translational level as well. Interestingly, protein deglycase DJ-1 (an antioxidative protein) showed an increase in its messenger RNA (mRNA) expression in both MM1 and VV2 subtypes but protein expression only in VV2 subtype in cerebellum of sCJD patients. Nuclear translocalization of DJ-1 confirmed its expressional alteration due to OS in sCJD. Downstream experiments showed the activation of nuclear factor erythroid-2 related factor 2 (Nrf2)/antioxidative response element (ARE) pathway. DJ-1 protein concentration was significantly increased during the clinical phase in cerebrospinal fluid of sCJD patients and also at presymptomatic and symptomatic stages in cerebellum of humanized PrP transgenic mice inoculated with sCJD (MM1 and VV2) brain. These results suggest the implication of oxidative stress during the pathophysiology of sCJD.

Proteomics applications in prion biology and structure

Prion diseases are a heterogeneous class of fatal neurodegenerative disorders associated with misfolding of host cellular prion protein (PrP(C)) into a pathological isoform, termed PrP(Sc). Prion diseases affect various mammals, including humans, and effective treatments are not available. Prion diseases are distinguished from other protein misfolding disorders - such as Alzheimer's or Parkinson's disease - in that they are infectious. Prion diseases occur sporadically without any known exposure to infected material, and hereditary cases resulting from rare mutations in the prion protein have also been documented. The mechanistic underpinnings of prion and other neurodegenerative disorders remain poorly understood. Various proteomics techniques have been instrumental in early PrP(Sc) detection, biomarker discovery, elucidation of PrP(Sc) structure and mapping of biochemical pathways affected by pathogenesis. Moving forward, proteomics approaches will likely become more integrated into the clinical and research settings for the rapid diagnosis and characterization of prion pathogenesis.

Behavioral abnormalities in prion protein knockout mice and the potential relevance of PrP(C) for the cytoskeleton

The cellular prion protein (PrP(C)) is a highly conserved protein, which is anchored to the outer surface of the plasma membrane. Even though its physiological function has already been investigated in different cell or mouse models where PrP(C) expression is either upregulated or depleted, its exact physiological role in a mammalian organism remains elusive. Recent studies indicate that PrP(C) has multiple functions and is involved in cognition, learning, anxiety, locomotion, depression, offensive aggression and nest building behavior. While young animals (3 months of age) show only marginal abnormalities, most of the deficits become apparent as the animals age, which might indicate its role in neurodegeneration or neuroprotection. However, the exact biochemical mechanism and signal transduction pathways involving PrP(C) are only gradually becoming clearer. We report the observations made in different studies using different Prnp0/0 mouse models and propose that PrP(C) plays an important role in the regulation of the cytoskeleton and associated proteins. In particular, we showed a nocodazole treatment influenced colocalization of PrP(C) and α tubulin 1. In addition, we confirmed the observed deficits in nest building using a different backcrossed Prnp0/0 mouse line.

Creutzfeldt-Jakob Disease Subtype-Specific Regional and Temporal Regulation of ADP Ribosylation Factor-1-Dependent Rho/MLC Pathway at Pre-Clinical Stage

Small GTPases of the Arf family mainly activate the formation of coated carrier vesicles. We showed that class-I Arf1 interacts specifically with full length GPI-anchored cellular prion protein (PrP(C)). Several recent reports have also demonstrated a missing link between the endoplasmic reticulum and the Golgi-complex role for proper folding, but the exact molecular mechanism is not yet fully understood. In the present study, we identified and characterized the interactive role of Arf1 during PrP(C) intracellular distribution under pathophysiological conditions. PrP(C) interaction with Arf1 was investigated in cortical primary neuronal cultures of PrP(C) wild type and knockout mice (PrP(-/-)). Arf1 and PrP(C) co-binding affinity was confirmed using reverse co-immunoprecipitation, co-localization affinity using confocal laser-scanning microscopy. Treatment with brefeldin-A modulated Arf1 expression and resulted in down-regulation and redistribution of PrP(C) into cytosolic region. In the pre-symptomatic stage of the disease, Arf1 expression was significantly downregulated in the frontal cortex in tg340 mice expressing about fourfold of human PrP-M129 with PrP null background that had been inoculated with human sCJD MM1 brain tissue homogenates (sCJD MM1 mice). In addition, the frontal cortex of CJD human brain demonstrated significant binding capacity of Arf1 protein using co-immunoprecipitation analysis. We also examined Arf1 expression in the brain of CJD patients with the subtypes MM1 and VV2 and found that it was regulated in a region-specific manner. In the frontal cortex, Arf1 expression was not significantly changed in either MM1 or VV2 subtype. Interestingly, Arf1 expression was significantly reduced in the cerebellum in both subtypes as compared to controls. Furthermore, we observed altered RhoA activity, which in turn affects myosin light-chain (MLC) phosphorylation and Arf1-dependent PI3K pathway. Together, our findings underscore a key early symptomatic role of Arf1 in neurodegeneration. Targeting the Arf/Rho/MLC signaling axis might be a promising strategy to uncover the missing link which probably influences disease progression and internal homeostasis of misfolded proteins.

Applying the tools of chemistry (mass spectrometry and covalent modification by small molecule reagents) to the detection of prions and the study of their structure

Prions are molecular pathogens, able to convert a normal cellular prion protein (PrP(C)) into a prion (PrP(Sc)). The information necessary for this conversion is contained in the conformation of PrP(Sc). Mass spectrometry (MS) and small-molecule covalent reactions have been used to study prions. Mass spectrometry has been used to detect and quantitate prions in the attomole range (10⁻¹⁸ mole). MS-based analysis showed that both possess identical amino acid sequences, one disulfide bond, a GPI anchor, asparagine-linked sugar antennae, and unoxidized methionines. Mass spectrometry has been used to define elements of the secondary and tertiary structure of wild-type PrP(Sc) and GPI-anchorless PrP(Sc). It has also been used to study the quaternary structure of the PrP(Sc) multimer. Small molecule reagents react differently with the same lysine in the PrP(C) conformation than in the PrP(Sc) conformation. Such differences can be detected by Western blot using mAbs with lysine-containing epitopes, such as 3F4 and 6D11. This permits the detection of PrP(Sc) without the need for proteinase K pretreatment and can be used to distinguish among prion strains. These results illustrate how two important chemical tools, mass spectrometry and covalent modification by small molecules, are being applied to the detection and structural study of prions. Furthermore these tools are or can be applied to the study of the other protein misfolding diseases such as Alzheimer Disease, Parkinson Disease, or ALS.

Prion protein (PrP) gene-knockout cell lines: insight into functions of the PrP

Elucidation of prion protein (PrP) functions is crucial to fully understand prion diseases. A major approach to studying PrP functions is the use of PrP gene-knockout (Prnp (-/-)) mice. So far, six types of Prnp (-/-) mice have been generated, demonstrating the promiscuous functions of PrP. Recently, other PrP family members, such as Doppel and Shadoo, have been found. However, information obtained from comparative studies of structural and functional analyses of these PrP family proteins do not fully reveal PrP functions. Recently, varieties of Prnp (-/-) cell lines established from Prnp (-/-) mice have contributed to the analysis of PrP functions. In this mini-review, we focus on Prnp (-/-) cell lines and summarize currently available Prnp (-/-) cell lines and their characterizations. In addition, we introduce the recent advances in the methodology of cell line generation with knockout or knockdown of the PrP gene. We also discuss how these cell lines have provided valuable insights into PrP functions and show future perspectives.