Plasmid-reprogramming of human fibroblasts
By onThis protocol is part of a collection of protocols for the paper, "Glucocerebrosidase, a Parkinson's disease-associated protein, is imported into mitochondria and regulates complex I assembly and function"
L1 retrotransposons drive human neuronal transcriptome complexity and functional diversification
By onThe genetic mechanisms underlying the expansion in size and complexity of the human brain remains poorly understood. L1 retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution is largely unknown. Using multi-omic profiling we here demonstrate that L1-promoters are dynamically active in the developing and adult human brain. L1s generate hundreds of developmentally regulated and cell-type specific transcripts, many which are co-opted as chimeric transcripts or regulatory RNAs. One L1-derived lncRNA, LINC01876, is a human-specific transcript expressed exclusively during brain development. CRISPRi-silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain.
LRRK2 kinase activity regulates GCase level and enzymatic activity differently depending on cell type in Parkinson’s disease
By onLeucine-rich repeat kinase 2 (LRRK2) is a kinase involved in different cellular functions, including autophagy, endolysosomal pathways, and immune function. Mutations in LRRK2 cause autosomal-dominant forms of Parkinson’s disease (PD). Heterozygous mutations in GBA1, the gene encoding the lysosomal enzyme glucocerebrosidase (GCase), are the most common genetic risk factors for PD. Moreover, GCase function is altered in idiopathic PD and in other genetic forms of the disease. Recent work suggests that LRRK2 kinase activity can regulate GCase function. However, both a positive and a negative correlation have been described. To gain insights into the impact of LRRK2 on GCase, we performed a comprehensive analysis of GCase levels and activity in complementary LRRK2 models, including (i) LRRK2 G2019S knock in (GSKI) mice, (ii) peripheral blood mononuclear cell (PBMCs), plasma, and fibroblasts from PD patients carrying LRRK2 G2019S mutation, (iii) patient iPSCs-derived neurons; (iv) endogenous and overexpressed cell models. In some of these models we found a positive correlation between the activities of LRRK2 and GCase, which was further confirmed in cell lines with genetic and pharmacological manipulation of LRRK2 kinase activity. GCase protein level is reduced in GSKI brain tissues and in G2019S iPSCs-derived neurons, but increased in fibroblasts and PBMCs from patients, suggesting cell-type-specific effects. Overall, our study indicates that LRRK2 kinase activity affects both the levels and the catalytic activity of GCase in a cell-type-specific manner, with important implications in the context of therapeutic application of LRRK2 inhibitors in GBA1-linked and idiopathic PD.
Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function
By onRaw data files used for the manuscript "Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function" https://www.researchsquare.com/article/rs-1521848/v1
Bulk RNA sequencing analysis
By onThis protocol describes the steps for the bioinformatical analysis of bulk RNA sequencing with a focus on evolutionary young L1s.
Collection of protocols of Team Deleidi used in the publication: “”LRRK2 kinase activity regulates GCase level and enzymatic activity differently depending on cell type in Parkinson’s disease””
By onCollection of protocols of Team Deleidi used in the publication: ""LRRK2 kinase activity regulates GCase level and enzymatic activity differently depending on cell type in Parkinson’s disease""
The GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines.
By onThe GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines (associated with publication 10.1101/2022.06.01.494130).
Validation of Genotyping Method for L444P Mice Ear-Clips.
By on|| Team Schapira || Authors Revi Shahar Golan, David ChauAbstractAim: the genotyping is used to identify if mice are heterozygote (hetero) or Wild-Type (WT), and the aim of the work is to validate the digestion method, and PCR program, the PCR primers, and the interpretation of the results. Associated with publication: doi: 10.1093/brain/awx221
The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1
By onThe authors identify novel transcripts from both GBA1 and GBAP1, including protein-coding transcripts that are translated in vitro and detected in proteomic data, but that lack GCase activity.
Sex-specific microglial responses to glucocerebrosidase inhibition
By onMorpho-dynamic analysis occurring in primary cells derived from female and male mice in response to proinflammatory stimulations and glucocerebrosidase inhibition.
Evaluation of an adapted semi-automated DNA extraction for human salivary shotgun metagenomics
By onThis study demonstrates that the authors’ semi-automated protocol is suitable for shotgun metagenomic analysis.
Microbes and Parkinson’s Disease: from associations to mechanisms
By onSeveral microbes, including viruses, bacteria, and fungi, have been associated with an increased risk of PD in humans. Microbial infections can induce similar common pathways that are associated with PD, including systemic inflammatory responses, α-synuclein misfolding, and disruption of mitochondria. PD-associated gene mutations can impact host–microbe interactions, suggesting that even familial forms of PD may be influenced by microbes.
Sphingolipid changes in Parkinson L444P GBAmutation fibroblasts promote α-synuclein aggregation
By onIntraneuronal accumulation of aggregated α-synuclein is a pathological hallmark of Parkinson’s disease. Therefore, mechanisms capable of promoting α-synuclein deposition bear important pathogenetic implications. Mutations of the glucocerebrosidase 1 (GBA) gene represent a prevalent Parkinson’s disease risk factor. They are associated with loss of activity of a key enzyme involved in lipid metabolism, glucocerebrosidase, supporting a mechanistic relationship between abnormal α-synuclein–lipid interactions and the development of Parkinson pathology. In this study, the lipid membrane composition of fibroblasts isolated from control subjects, patients with idiopathic Parkinson’s disease and Parkinson's disease patients carrying the L444P GBA mutation (PD-GBA) was assayed using shotgun lipidomics. The lipid profile of PD-GBA fibroblasts differed significantly from that of control and idiopathic Parkinson’s disease cells. It was characterized by an overall increase in sphingolipid levels. It also featured a significant increase in the proportion of ceramide, sphingomyelin and hexosylceramide molecules with shorter chain length and a decrease in the percentage of longer-chain sphingolipids. The extent of this shift was correlated to the degree of reduction of fibroblast glucocerebrosidase activity. Lipid extracts from control and PD-GBA fibroblasts were added to recombinant α-synuclein solutions. The kinetics of α-synuclein aggregation were significantly accelerated after addition of PD-GBA extracts as compared to control samples. Amyloid fibrils collected at the end of these incubations contained lipids, indicating α-synuclein–lipid co-assembly. Lipids extracted from α-synuclein fibrils were also analysed by shotgun lipidomics. Data revealed that the lipid content of these fibrils was significantly enriched by shorter-chain sphingolipids. In a final set of experiments, control and PD-GBA fibroblasts were incubated in the presence of the small molecule chaperone ambroxol. This treatment restored glucocerebrosidase activity and sphingolipid levels and composition of PD-GBA cells. It also reversed the pro-aggregation effect that lipid extracts from PD-GBA fibroblasts had on α-synuclein. Taken together, the findings of this study indicate that the L444P GBA mutation and consequent enzymatic loss are associated with a distinctly altered membrane lipid profile that provides a biological fingerprint of this mutation in Parkinson fibroblasts. This altered lipid profile could also be an indicator of increased risk for α-synuclein aggregate pathology.
x4 GBA Plasmids
By onThe below plasmids are deposited and available via Addgene:https://www.addgene.org/Anthony_Schapira/ . These have been used in publication: 10.1093/hmg/ddac233 188580 WT GBA pcDNA3.1 GBA (Homo sapiens) 188581 E326K GBA pcDNA3.1 GBA (Homo sapiens) 188582 L444P GBA pcDNA3.1 GBA (Homo sapiens) 188583 N370S GBA pcDNA3.1 GBA (Homo sapiens)
Post mortem human substantial nigra TH staining
By onThis protocol is standardized for postmortem (frozen) SN tissue from pathologically diagnosed PD patients and control individuals for Immunofluorescence staining.
Phenotypic effect of GBA1 variants in individuals with and without Parkinson disease: the RAPSODI study
By onThe authors’ results support previous evidence that GBA1-positive PD has a specific phenotype with more severe non-motor symptoms. The authors did not reproduce previous findings of more frequent prodromal PD signs in non-affected GBA1 carriers.
Unilateral intranigral AAV alpha synuclein mouse model
By onAs some protocols have not been made public and are only shared within the network, you may need to login to the protocols.io to view the link.Don’t have a login? Use this special invite link and click join to get started. Click here for detailed instructions on how to set up your free account and view all protocols.
Intracellular Cytokine (ICS) Staining Protocol
By onThis protocol details about intracellular cytokine (ICS) staining.
