All-trans retinoic acid down-regulates prion protein expression independently of granulocyte maturation

An arrayed genome-wide perturbation screen identifies the ribonucleoprotein Hnrnpk as rate-limiting for prion propagation

A defining characteristic of mammalian prions is their capacity for self-sustained propagation. Theoretical considerations and experimental evidence suggest that prion propagation is modulated by cell-autonomous and non-autonomous modifiers. Using a novel quantitative phospholipase protection assay (QUIPPER) for high-throughput prion measurements, we performed an arrayed genome-wide RNA interference (RNAi) screen aimed at detecting cellular host-factors that can modify prion propagation. We exposed prion-infected cells in high-density microplates to 35,364 ternary pools of 52,746 siRNAs targeting 17,582 genes representing the majority of the mouse protein-coding transcriptome. We identified 1,191 modulators of prion propagation. While 1,151 modified the expression of both the pathological prion protein, PrP^Sc , and its cellular counterpart, PrP^C , 40 genes selectively affected PrP^Sc . Of the latter 40 genes, 20 augmented prion production when suppressed. A prominent limiter of prion propagation was the heterogeneous nuclear ribonucleoprotein Hnrnpk. Psammaplysene A (PSA), which binds Hnrnpk, reduced prion levels in cultured cells and protected them from cytotoxicity. PSA also reduced prion levels in infected cerebellar organotypic slices and alleviated locomotor deficits in prion-infected Drosophila melanogaster expressing ovine PrP^C . Hence, genome-wide QUIPPER-based perturbations can discover actionable cellular pathways involved in prion propagation. Further, the unexpected identification of a prion-controlling ribonucleoprotein suggests a role for RNA in the generation of infectious prions.

Novel regulators of PrPC biosynthesis revealed by genome-wide RNA interference

The cellular prion protein PrP^C is necessary for prion replication, and its reduction greatly increases life expectancy in animal models of prion infection. Hence the factors controlling the levels of PrP^C may represent therapeutic targets against human prion diseases. Here we performed an arrayed whole-transcriptome RNA interference screen to identify modulators of PrP^C expression. We cultured human U251-MG glioblastoma cells in the presence of 64’752 unique siRNAs targeting 21’584 annotated human genes, and measured PrP^C using a one-pot fluorescence-resonance energy transfer immunoassay in 51’128 individual microplate wells. This screen yielded 743 candidate regulators of PrP^C. When downregulated, 563 of these candidates reduced and 180 enhanced PrP^C expression. Recursive candidate attrition through multiple secondary screens yielded 54 novel regulators of PrP^C, 9 of which were confirmed by CRISPR interference as robust regulators of PrP^C biosynthesis and degradation. The phenotypes of 6 of the 9 candidates were inverted in response to transcriptional activation using CRISPRa. The RNA-binding post-transcriptional repressor Pumilio-1 was identified as a potent limiter of PrP^C expression through the degradation of PRNP mRNA. Because of its hypothesis-free design, this comprehensive genetic-perturbation screen delivers an unbiased landscape of the genes regulating PrP^C levels in cells, most of which were unanticipated, and some of which may be amenable to pharmacological targeting in the context of antiprion therapies.

The cellular prion protein (PrP^C) acts as both, the substrate for prion formation and mediator of prion toxicity during the progression of all prion diseases. Suppressing the levels of PrP^C is a viable therapeutic strategy as PRNP null animals are resistant to prion disease and the knockout of PRNP is not associated with any severe phenotypes. Motivated by the scarcity of knowledge regarding the molecular regulators of PrP^C biosynthesis and degradation, which might serve as valuable targets to control its expression, here, we present a cell-based genome wide RNAi screen in arrayed format. The screening effort led to the identification of 54 regulators, nine of which were confirmed by an independent CRISPR-based method. Among the final nine targets, we identified PUM1 as a regulator of PRNP mRNA by acting on the 3’UTR promoting its degradation. The newly identified factors involved in the life cycle of PrP^C provided by our study may also represent themselves as therapeutic targets for the intervention of prion diseases.

A 3-miRNA signature predicts prognosis of pediatric and adolescent cytogenetically normal acute myeloid leukemia

Acute myeloid leukemia is a hematologic malignancy with significant molecular heterogeneity. MicroRNAs have important biological functions and play critical roles in pathogenesis and prognosis in a variety of cancers including acute myeloid leukemia. Some reports have constructed risk stratification systems for adult acute myeloid leukemia patients using microRNAs to predict an optimal outcome of patients. However, little has been done in pediatric and adolescent patients. The purpose of this study is to identify a panel of microRNA signature that could predict prognosis in younger cytogenetically normal acute myeloid leukemia patients by analyzing the data from The Cancer Genome Atlas. A total of 59 cytogenetically normal acute myeloid leukemia patients under 21 years with corresponding clinical data were enrolled in our study. Using univariate Cox's model, we found 17 miRNAs were significantly related with overall survival in pediatric and adolescent cytogenetically normal acute myeloid leukemia patients but no clinical parameter was found significant related with overall survival. The multivariate Cox regression identified high expression of hsa-miR-146b was independent poor prognostic factor and high expression of hsa-miR-181c and hsa-miR-4786 appeared to be favorable factors. A model was proposed based on these three miRNAs. Leave-one-out Cross Validation method and Permutation Test was further used to evaluate this model. The function role of has-mir-181c was further studied by carrying out flow cytometry and cell counting kit-8 (CCK-8) in U937 cell line. The results indicate that the 3-microRNA-based signature is a reliable prognostic biomarker for pediatric and adolescent cytogenetically normal acute myeloid leukemia patients.

Nrf-2 regulation of prion protein expression is independent of oxidative stress

Cellular expression of host prion protein (PrP) is essential to infection with prion disease. Understanding the mechanisms that regulate prion protein expression at both the transcriptional and translational levels is therefore an important goal. The cellular prion protein has been associated with resistance to oxidative, and its expression is also increased by oxidative stress. The transcription factor Nrf-2 is associated with cellular responses to oxidative stress and is known to induce upregulation of antioxidant defense mechanisms. We have identified an Nrf-2 binding site in the prion protein promoter (Prnp) and shown that Nrf-2 downregulated PrP expression. However, this effect is independent of oxidative stress as oxidative stress can up-regulate PrP expression regardless of the level of Nrf-2 expression. Furthermore, Nrf-2 has no impact on PrP expression when cells are infected with scrapie. These findings highlight that Nrf-2 can regulate PrP expression, but that this regulation becomes uncoupled during cellular stress.

RARB and STMN2 polymorphisms are not associated with sporadic Creutzfeldt-Jakob disease (CJD) in the Korean population

Polymorphisms in the prion protein gene (PRNP) can affect the susceptibility of humans to prion diseases. Recently, aside from PRNP, single nucleotide polymorphisms (SNPs) of two candidate genes for susceptibility to human prion diseases have been identified by human genome-wide association studies (GWAS) in the British population. One SNP of retinoic acid receptor beta (RARB), which is correlated with prion disease incubation time in mice, was associated with human prion diseases such as variant and iatrogenic CJD in the British population. The other SNP of the gene that encodes SCG10 (STMN2), which is related to clinical onset of sporadic CJD, was also associated with variant CJD and kuru. In order to investigate whether two polymorphisms located in upstream of RARB and STMN2 are associated with sporadic CJD in the Korean population, we compared genotype and allele frequencies of these polymorphisms in 217 sporadic CJD patients and 216 healthy Koreans. The genotype distribution and allele frequencies in upstream of the RARB and STMN2 polymorphisms were not significantly different between healthy controls and Korean sporadic CJD patients. This finding indicates that the two SNPs are not correlated with genetic susceptibility to sporadic CJD in the Korean population. This is the first genetic association study of RARB and STMN2 with sporadic CJD in an Asian population.

Modelling neurodegeneration in prion disease - applications for drug development

Prion diseases are a group of neurodegenerative diseases that affect mammals, including humans and ruminants such as sheep. They are believed to be caused by the conversion of the prion protein (PrP), a host expressed protein, into a toxic form (PrP(sc)). PrP(sc) accumulates in the brain, resulting in neuronal loss and the typical spongiform appearance of the brain. So far, there are no effective therapies available for prion diseases. This review discusses possible therapies for prion diseases and the models available for advancing research into the disease.

Gene regulation as a potential avenue for the treatment of neurodegenerative disorders

BACKGROUND

As more people live to an older age, the frequency of diseases associated with longer life begins to increase. Neurodegenerative disorders are the worst of these in that there is now no treatment that offers any real improvement. For this reason, any new avenue of research that could lead to a treatment needs to be rigorously pursued. In many cases, neurodegenerative diseases are associated with the expression of a protein with an altered conformation or that generates a breakdown product associated with the cause. Clearly, the prevention of this process is a key therapeutic target.

OBJECTIVE

In this review, the potential for regulating gene expression to prevent or reverse neurodegenerative disease is explored.

CONCLUSIONS

Whereas much research has been directed at the proteins associated with neurodegeneration, understanding what controls their expression presents a new way this issue could be studied.

Functional genomics approach for identification of molecular processes underlying neurodegenerative disorders in prion diseases

Prion diseases or transmissible spongiform encephalopathies (TSEs) are infectious neurodegenerative disorders leading to death. These include Cresutzfeldt-Jakob disease (CJD), familial, sporadic and variant CJD and kuru in humans; and animal TSEs include scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle, chronic wasting disease (CWD) of mule deer and elk, and transmissible mink encephalopathy. All these TSEs share common pathological features such as accumulation of mis-folded prion proteins in the central nervous system leading to cellular dysfunction and cell death. It is important to characterize the molecular pathways and events leading to prion induced neurodegeneration. Here we discuss the impact of the functional genomics approaches including microarrays, subtractive hybridization and microRNA profiling in elucidating transcriptional cascades at different stages of disease. Many of these transcriptional changes have been observed in multiple neurodegenerative diseases which may aid in identification of biomarkers for disease. A comprehensive characterization of expression profiles implicated in neurodegenerative disorders will undoubtedly advance our understanding on neuropathology and dysfunction during prion disease and other neurodegenerative disorders. We also present an outlook on the future work which may focus on analysis of structural genetic variation, genome and transcriptome sequencing using next generation sequencing with an integrated approach on animal and human TSE related studies.

Prion disease and the innate immune system

Prion diseases or transmissible spongiform encephalopathies are a unique category of infectious protein-misfolding neurodegenerative disorders. Hypothesized to be caused by misfolding of the cellular prion protein these disorders possess an infectious quality that thrives in immune-competent hosts. While much has been discovered about the routing and critical components involved in the peripheral pathogenesis of these agents there are still many aspects to be discovered. Research into this area has been extensive as it represents a major target for therapeutic intervention within this group of diseases. The main focus of pathological damage in these diseases occurs within the central nervous system. Cells of the innate immune system have been proven to be critical players in the initial pathogenesis of prion disease, and may have a role in the pathological progression of disease. Understanding how prions interact with the host innate immune system may provide us with natural pathways and mechanisms to combat these diseases prior to their neuroinvasive stage. We present here a review of the current knowledge regarding the role of the innate immune system in prion pathogenesis.

Activation and repression of prion protein expression by key regions of intron 1

Expression of the prion protein is necessary for infection with prion diseases. Altered expression levels may play an important role in susceptibility to infection. Therefore, understanding the mechanisms that regulate prion protein expression is of great importance. It was previously shown that expression of the prion protein is to some degree regulated by an alternative promoter within intron 1. Studies using GFP and luciferase reporter systems were undertaken to determine key sites for the repression and activation of expression of the prion protein driven by intron 1. We identified a region within intron 1 sufficient to drive prion protein expression. Our findings highlight two potential repressor regions. Both regions have binding sites for the known repressor Hes-1. Hes-1 overexpression caused a dramatic decrease in PrP protein expression. Additionally, we have identified Atox-1 as a transcription factor that upregulates prion protein expression. These findings clearly indicate that intron 1 plays a key role in regulation of prion protein expression levels.

Genomic and post-genomic analyses of human prion diseases

Prion diseases share common features of neurodegenerative disorders, infectious diseases and pathologies linked to misfolded proteins. Whether these aspects are independently and fortuitously present in prion diseases or are somewhat linked together remains unsettled, but the contribution of genomic, proteomic, metabolomic and spectroscopic techniques might give insights into this puzzle, and likely give hope for therapy to patients. Although the prion protein gene (PRNP) governs most of the clinical and pathological features of prion diseases and plays a pivotal role in determining host susceptibility, there are still many uncertainties and unknown risk factors that need to be clarified and identified. Several genes, other than PRNP, have recently been found to be associated with a risk of developing sporadic or variant Creutzfeldt-Jakob disease, but these novel data have been produced in a relatively small number of patients and controls and, therefore, need further confirmation. The same criticism applies to the identification of the over 20 new cerebrospinal fluid or plasma markers of disease. Some of these markers seem related to the massive brain damage that occurs, rather than being specific to prion infection. Nevertheless, genomic and post-genomic approaches have shown that these techniques are very powerful, and the best way to overcome the scantiness of samples would be to encourage strong collaboration between different centers of excellence in prion diseases. In this review, we describe the most recent and outstanding advances offered by genomics and post-genomics analyses in the field of human prion diseases.

Genetic risk factors for variant Creutzfeldt-Jakob disease: a genome-wide association study

Background

Human and animal prion diseases are under genetic control, but apart from PRNP (the gene that encodes the prion protein), we understand little about human susceptibility to bovine spongiform encephalopathy (BSE) prions, the causal agent of variant Creutzfeldt–Jakob disease (vCJD).

Methods

We did a genome-wide association study of the risk of vCJD and tested for replication of our findings in samples from many categories of human prion disease (929 samples) and control samples from the UK and Papua New Guinea (4254 samples), including controls in the UK who were genotyped by the Wellcome Trust Case Control Consortium. We also did follow-up analyses of the genetic control of the clinical phenotype of prion disease and analysed candidate gene expression in a mouse cellular model of prion infection.

Findings

The PRNP locus was strongly associated with risk across several markers and all categories of prion disease (best single SNP [single nucleotide polymorphism] association in vCJD p=2·5×10⁻¹⁷; best haplotypic association in vCJD p=1×10⁻²⁴). Although the main contribution to disease risk was conferred by PRNP polymorphic codon 129, another nearby SNP conferred increased risk of vCJD. In addition to PRNP, one technically validated SNP association upstream of RARB (the gene that encodes retinoic acid receptor beta) had nominal genome-wide significance (p=1·9×10⁻⁷). A similar association was found in a small sample of patients with iatrogenic CJD (p=0·030) but not in patients with sporadic CJD (sCJD) or kuru. In cultured cells, retinoic acid regulates the expression of the prion protein. We found an association with acquired prion disease, including vCJD (p=5·6×10⁻⁵), kuru incubation time (p=0·017), and resistance to kuru (p=2·5×10⁻⁴), in a region upstream of STMN2 (the gene that encodes SCG10). The risk genotype was not associated with sCJD but conferred an earlier age of onset. Furthermore, expression of Stmn2 was reduced 30-fold post-infection in a mouse cellular model of prion disease.

Interpretation

The polymorphic codon 129 of PRNP was the main genetic risk factor for vCJD; however, additional candidate loci have been identified, which justifies functional analyses of these biological pathways in prion disease.

Funding

The UK Medical Research Council.

Physiology of the prion protein

Prion diseases are transmissible spongiform encephalopathies (TSEs), attributed to conformational conversion of the cellular prion protein (PrP(C)) into an abnormal conformer that accumulates in the brain. Understanding the pathogenesis of TSEs requires the identification of functional properties of PrP(C). Here we examine the physiological functions of PrP(C) at the systemic, cellular, and molecular level. Current data show that both the expression and the engagement of PrP(C) with a variety of ligands modulate the following: 1) functions of the nervous and immune systems, including memory and inflammatory reactions; 2) cell proliferation, differentiation, and sensitivity to programmed cell death both in the nervous and immune systems, as well as in various cell lines; 3) the activity of numerous signal transduction pathways, including cAMP/protein kinase A, mitogen-activated protein kinase, phosphatidylinositol 3-kinase/Akt pathways, as well as soluble non-receptor tyrosine kinases; and 4) trafficking of PrP(C) both laterally among distinct plasma membrane domains, and along endocytic pathways, on top of continuous, rapid recycling. A unified view of these functional properties indicates that the prion protein is a dynamic cell surface platform for the assembly of signaling modules, based on which selective interactions with many ligands and transmembrane signaling pathways translate into wide-range consequences upon both physiology and behavior.

Prion protein facilitates hormone-induced differentiation of mammary gland epithelial cells

Expression of prion protein has been reported for a variety of cell types including neuronal cells, haematopoietic stem cells, lymphocytes, fibroblasts, and epithelial cells. However, the characterization of the physiological roles exhibited by this protein is still in progress and multiple biological functions have been described to date. In this study we have characterized the contribution of prion protein during hormone-induced differentiation of mouse mammary gland epithelial cells. We present evidence that prion expression enhances the differentiation-capabilities of these cells indicating novel physiological roles during mammary gland development. In addition we were able to demonstrate the presence of prion molecules resistant to mild proteinase digestion in differentiated mammary gland epithelial cells. This represents the first report of proteinase-resistant prion proteins in a physiological, non-pathogenic context.

Regulation of prion protein expression by noncoding regions of the Prnp gene

Expression of the cellular prion protein is necessary for the transmission and propagation of prion diseases. Increasing the level of prion protein expression decreases the incubation period for these diseases. Therefore, understanding the regulation of prion protein expression could be critical for treating or preventing these diseases. We investigated the regulation of prion protein expression by the promoter and noncoding regions of the bovine and murine Prnp genes. We determined that expression is modulated by intron 1 and exon 1. In the absence of intron1, exon 1 inhibited activity of the promoter. However, intron 1 demonstrated promoter-like activity and possessed a TATA box. In addition, we identified an alternative transcript present in the brains of cattle and mice that lacks exon 1. Taken together, these results show that intron 1 and exon 1 play a critical role in the regulation of prion protein expression. Because switching off prion protein expression has been shown to arrest prion disease, these regions present novel targets for intervention in the disease process.

Efficacy of gemtuzumab ozogamicin on ATRA- and arsenic-resistant acute promyelocytic leukemia (APL) cells

Acute promyelocytic leukemia (APL) cells express a considerable level of CD33, which is a target of gemtuzumab ozogamicin (GO), and a significantly lower level of P-glycoprotein (P-gp). In this study, we examined whether GO was effective on all-trans retinoic acid (ATRA)- or arsenic trioxide (ATO)-resistant APL cells. Cells used were an APL cell line in which P-gp was undetectable (NB4), ATRA-resistant NB4 (NB4/RA), NB4 and NB4/RA that had been transfected with MDR-1 cDNA (NB4/MDR and NB4/RA/MDR, respectively), ATO-resistant NB4 (NB4/As) and blast cells from eight patients with clinically ATRA-resistant APL including two patients with ATRA- and ATO-resistant APL. The efficacy of GO was analyzed by (3)H-thymidine incorporation, the dye exclusion test and cell cycle distribution. GO suppressed the growth of NB4, NB4/RA and NB4/As cells in a dose-dependent manner. GO increased the percentage of hypodiploid cells significantly in NB4, NB4/RA and NB4/As cells, and by a limited degree in NB4/MDR and NB4/RA/MDR cells. Similar results were obtained using blast cells from the patients with APL. GO is effective against ATRA- or ATO-resistant APL cells that do not express P-gp, and the mechanism of resistance to GO is not related to the mechanism of resistance to ATRA or ATO in APL cells. Leukemia (2005) 19, 1306-1311. doi:10.1038/sj.leu.2403807; published online 26 May 2005.

Does transmissibility necessarily imply infectivity in spongiform encephalopathy?

The essential biologic properties inherently acquired subsequent to conformational transformation of the alpha-helical molecular structure of the normal cellular PrPc isoform to the beta-sheet molecular tertiary structure of the abnormal PrPsc associated with a rapidly spreading form of neuronal cell death of spongiform encephalopathy are unknown. However, the vacuolization that chiefly characterizes the morphology of neurons in spongiform encephalopathy might constitute a physical disruption with subsequent rapidly progressive impairment of maintenance of homeostatic viability of neurons due to precisely loss of membrane integrity of the plasmalemma and cell organelles. As far as transmission of the prion particle is concerned, it would appear that active incorporation of this agent under the direction of the affected neuronal cell itself would implicate host attributes as paramount factors determining not only susceptibility to the pathologic effects of the prion particle but also to the mode of such infliction as arising in and constituting spongiform encephalopathy beyond its acquisition and progression. As a single set of acquired circumstances determining both transmissibility and also pathologic lesion creation, the spongiform neuronal change might arise directly from a membrane abnormality of water ingress and egress in and out of the neuron. An excess of water ingress intra-neuronally might actually constitute a phenomenon of active lesion induction even in terms simply of biophysical stress intra-neuronally. In simple terms, an understanding of pathogenesis in spongiform encephalopathy might actually implicate aspects of transmissibility as direct attributes of processes of template replication within a system of utilization and elimination of the prion particle. Indeed, susceptibility to spongiform change might constitute one aspect of a biologic process that arises from conformational change of the prion protein molecule that would in turn result from variable polymorphisms in modes of reactive handling of PrPc and PrPsc by the neurons and other constituent cell elements in the central nervous system.