Iso-Seq mapping to L1HS/PA2 consensus sequence
By onThe protocol describes the steps to map HiFi reads to a consensus sequence and retrieve density plots.
Single cell/nuclei RNAseq analysis
By onThis protocol describes the process for the single cell/nuclei RNA sequencing data of the manuscript "L1retrotransposons drive human neuronal transcriptome complexity and functional diversification " from fetal forebrain and adult prefrontal cortex tissue.
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 fibroblasts.
DOPA pheomelanin is increased in nigral neuromelanin of Parkinson’s disease
By onNeuromelanin in the substantia nigra may be a key factor contributing to dopaminergic neuron vulnerability in Parkinson’s disease. Here, the authors investigated the relative composition and specific roles of pheomelanin and eumelanin in PD.
A prebiotic diet modulates microglia response and motor deficits in α-synuclein overexpressing mice
By onSingle-cell RNA-seq analysis of microglia from the substantia nigra and striatum uncovers increased pro-inflammatory signaling and reduced homeostatic responses in ASO mice compared to wild-type counterparts on standard diets. However, prebiotic feeding reverses pathogenic microglial states in ASO mice and promotes expansion of protective disease-associated macrophage (DAM) subsets of microglia. Notably, depletion of microglia using a CSF1R inhibitor eliminates the beneficial effects of prebiotics by restoring motor deficits to ASO mice despite feeding a prebiotic diet. These studies uncover a novel microglia-dependent interaction between diet and motor symptoms in mice, findings that may have implications for neuroinflammation and PD.
Single cell analysis of iPSC-derived midbrain organoids
By onThe following script was used for analysis of gene corrected (GC) versus GBA1 mutant (MUT) midbrain organoids. The purpose was to combine, filter, integrate, and identify clusters and differentially expressed genes sets. This is part of a Collection of protocols (dx.doi.org/10.17504/protocols.io.8epv593dng1b/v1) for the paper "Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function" (https://doi.org/10.21203/rs.3.rs-1521848/v1)
Subcellular and regional localization of mRNA translation in midbrain dopamine neurons
By onUsing, highly sensitive ribosome-bound RNA sequencing and imaging to characterize the translatome, the authors uncovered local mRNA translation of dopamine synthesis, release, and reuptake machinery in dendrites, but not axons.
Immunohistochemistry using paraffin embedded tissue
By onImmunohistochemistry using paraffin embedded tissue
qPCR of α-synuclein, TNF and NF-κβ
By onA procedure for quantitative real time reverse transcription PCR of α-synuclein, TNF, and NF-κβ.
Datasets associated with “Peripheral Neuronal Activation Shapes the Microbiome and Alters Gut Physiology”
By onDataset associated with the publication "Peripheral Neuronal Activation Shapes the Microbiome and Alters Gut Physiology"
Immunohistochemistry (IHC)
By onImmunohistochemistry for Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain.
Activation Induced Marker (AIM) Staining Protocol
By onThis protocol details about activation induced marker staining.
Generation of induced pluripotent stem cells and gene correction
By oniPSC generation and gene correction (CRISPR-CAS9) protocol.
Collection of protocols for paper: “Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function”
By onThis is a collection of protocols used in a recent preprint by the Deleidi Lab, Team Schapira. You can access pre-print at https://doi.org/10.21203/rs.3.rs-1521848/v1
Fluorescence in situ hybridization (FISH)
By onFluorescence in situ hybridization (FISH) in Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain
R code for paper Phenotype of GBA1 variants in individuals with and without Parkinson disease: the RAPSODI study
By onThis is the R code used to produce the results described in the paper "Phenotype of GBA1 variants in individuals with and without Parkinson’s disease: The RAPSODI study"
Complex I activity assay
By onThis protocol is part of a Collection of protocols (dx.doi.org/10.17504/protocols.io.8epv593dng1b/v1) for the paper "Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function" (https://doi.org/10.21203/rs.3.rs-1521848/v1)
Targeting the GBA1 pathway to slow Parkinson disease: Insights into clinical aspects, pathogenic mechanisms and new therapeutic avenues
By onThe GBA1 gene encodes the lysosomal enzyme glucocerebrosidase (GCase), which is involved in sphingolipid metabolism. Biallelic variants in GBA1 cause Gaucher disease (GD), a lysosomal storage disorder characterised by loss of GCase activity and aberrant intracellular accumulation of GCase substrates. Carriers of GBA1 variants have an increased risk of developing Parkinson disease (PD), with odds ratio ranging from 2.2 to 30 according to variant severity. GBA1 variants which do not cause GD in homozygosis can also increase PD risk. Patients with PD carrying GBA1 variants show a more rapidly progressive phenotype compared to non-carriers, emphasising the need for disease modifying treatments targeting the GBA1 pathway. Several mechanisms secondary to GCase dysfunction are potentially responsible for the pathological changes leading to PD. Misfolded GCase proteins induce endoplasmic reticulum stress and subsequent unfolded protein response and impair the autophagy-lysosomal pathway. This results in α-synuclein accumulation and spread, and promotes neurodegenerative changes. Preclinical evidence also shows that products of GCase activity can promote accumulation of α-synuclein, however there is no convincing evidence of substrate accumulation in GBA1-PD brains. Altered lipid homeostasis secondary to loss of GCase activity could also contribute to PD pathology. Treatments that target the GBA1 pathway could reverse these pathological processes and halt/slow the progression of PD. These range from augmentation of GCase activity via GBA1 gene therapy, restoration of normal intracellular GCase trafficking via molecular chaperones, and substrate reduction therapy. This review discusses the pathways associated with GBA1-PD and related novel GBA1-targeted interventions for PD treatment.
Fecal metagenomic sequencing data for PD patients and controls from Rush University Medical Center
By onFecal metagenomic sequencing data associated with Boktor et al. (2023). This dataset includes samples from the Rush University Medical Center cohort.