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  • Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures–Fluorospot SFC

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    Fluorospot SFC (combined IFNg, IL-5, and IL-10) data and corresponding HC-PD group IDs described in "Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures"

  • Subcellular and regional localization of mRNA translation in midbrain dopamine neurons–DropSeqPipeline8

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    This is a data processing pipeline for analyzing microwell- or DropSeq-like scRNA-seq data. It can also be used for analyzing pooled plate-based scRNA-seq

  • Differentiation NPCs to Dopaminergic/Midbrain Neurons

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    This protocol details methods for differentiation of NPCs to Dopaminergic/Midbrain Neurons. This 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)

  • A Single-Cell Atlas of Cell Types, States, and Other Transcriptional Patterns from Nine Regions of the Adult Mouse Brain

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    We report 690K single-cell transcriptomes from nine different brain regions from adult mice (Frontal and Posterior Cortex, Hippocampus, Thalamus, Cerebellum, Striatum, Globus Pallidus externus/Nucleus Basalis, Entopeduncular / Subthalamic Nuclei, & Substantia Nigra / Ventral Tegmental Area).

  • Gcase co-immunoprecipitation

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    The authors developed this protocol to identify protein-protein interactions between the enzyme glucocerebrosidase (GCase) and other proteins in human iPSC-derived Neural Precursor Cells.

  • Axonal and somatodendritic proteomes of dopamine neurons in the mouse brain

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    Dopamine (DA) neurons modulate neural circuits and behaviors via dopamine release from expansive, long range axonal projections. The elaborate cytoarchitecture of DA neurons is embedded within complex brain tissues, making it difficult to access the DA neuronal proteome using conventional methods. Here, we demonstrate APEX2 proximity labeling within genetically targeted neurons in the mouse brain, enabling subcellular proteomics with cell type-specificity. By combining APEX2 biotinylation with mass spectrometry, we mapped the somatodendritic and axonal proteomes of DA neurons. Our dataset reveals the proteomic architecture underlying axonal transport, dopamine transmission, and axonal metabolism in DA neurons. We find a significant enrichment of proteins encoded by Parkinson’s disease-linked genes in dopaminergic axons, including proteins with previously undescribed axonal localization. Our proteomic datasets comprise a significant resource for axonal and DA neuronal cell biology, while the methodology developed here will enable future studies of other neural cell types. This mass spectrometry proteomics dataset is a part of "Subcellular proteomics of dopamine neurons in the mouse brain" (Hobson et. al, 2022)

  • Flag co-immunoprecipitation

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    Protocol used to pull down V5-FLAG-Gcase interacting proteins in HEK cells

  • Midbrain organoid generation from mfNPC

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    Optimised midbrain organoid generation from mfNPC.

  • Dopamine transporter and synaptic vesicle sorting defects underlie auxilin-associated Parkinson’s disease

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    Auxilin participates in clathrin uncoating to facilitate presynaptic endocytosis. Loss-of-function mutations of auxilin (PARK19) cause Parkinson’s disease. Using auxilin KO mice, Vidyadhara et al. (2023) show that synaptic vesicle sorting deficits, cytoplasmic dopamine accumulation, dopamine transporter mistrafficking, and synaptic autophagic overload may lead to pathogenesis of Parkinson’s disease in PARK19 patients. This file contains the data set used to generate all the main figures.

  • A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data

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    Single-cell RNA-sequencing technology enables the identification of cell-type-specific differential gene expressions. MARBLES, a new statistical model, effectively detects DE genes across conditions.

  • Peripheral neuronal activation shapes the microbiome and alters gut physiology

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    The authors specifically activate ChAT- or TH-expressing gut-associated neurons in mice and perform multi-omics, finding that subsets of peripherally-activated neurons differentially regulate the gut microbiome and host GI physiology.

  • Neurite_FISH_Quant–Python code for quantification of FISH puncta in neurites

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    This repository contains Jupyter Notebooks with Python 3 code for quantification of FISH puncta within neuronal dendrites or axons. However, prior identification of FISH puncta in the images (and optional neurite segmentation) is required. We use ImageJ plugins for this purpose, as specified below. The workflow assumes Z-stack, multi-channel fluorescence images, with one channel used for identification of neurites and other channels for FISH.

  • Determination of NM Concentration

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    This is the protocol for determining neuromelanin concentration and data.

  • Immunofluorescent staining for neuronal marker MAP2

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    This is the protocol for immunofluorescent staining for neuronal marker MAP2.

  • Expansion Microscopy

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    Expansion microscopy is a technique to visualize biological structures with higher spatial resolution than traditional microscopy methods.

  • Human neuroblastoma cell line SH-SY5Y culturing

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    This is the brief protocol for seeding and culturing human neuroblastoma SH-SY5Y cells.

  • Live-cell imaging

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    Live-cell imaging is a technique to visualize dynamic cellular processes in living biological samples.

  • Parkinson’s disease and cancer: a systematic review and meta-analysis of over 17 million participants

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    The authors examined risk association between Parkinson’s disease and cancer using data from 63 publications. With the exception of melanoma, the authors found that the risk association of Parkinson’s disease and cancer was inversely related.

  • Mitochondrial complex activity assays

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    Mitochondria complex activity assays measure the activity levels of the different complexes of the mitochondrial electron transport chain (ETC).

  • Dopamine transporter and synaptic vesicle sorting defects underlie auxilin-associated Parkinson’s disease

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    Auxilin participates in the uncoating of clathrin-coated vesicles (CCVs), thereby facilitating synaptic vesicle (SV) regeneration at presynaptic sites. Auxilin (DNAJC6/PARK19) loss-of-function mutations cause early-onset Parkinson's disease (PD). Here, we utilized auxilin knockout (KO) mice to elucidate the mechanisms through which auxilin deficiency and clathrin-uncoating deficits lead to PD. Auxilin KO mice display cardinal features of PD, including progressive motor deficits, α-synuclein pathology, nigral dopaminergic loss, and neuroinflammation. Significantly, treatment with L-DOPA ameliorated motor deficits. Unbiased proteomic and neurochemical analyses of auxilin KO brains indicated dopamine dyshomeostasis. We validated these findings by demonstrating slower dopamine reuptake kinetics in vivo, an effect associated with dopamine transporter misrouting into axonal membrane deformities in the dorsal striatum. Defective SV protein sorting and elevated synaptic autophagy also contribute to ineffective dopamine sequestration and compartmentalization, ultimately leading to neurodegeneration. This study provides insights into how presynaptic endocytosis deficits lead to dopaminergic vulnerability and pathogenesis of PD.

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