Catalog

ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We’ve created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.

Article

Integrated multi-cohort analysis of the Parkinson’s disease gut metagenome

Preprint: Here, the fecal metagenomes of those living with PD compared to others in the household were profiled from 4 geographically-distinct sites across 3 continents. The question was whether there were any specific PD-associated signatures in gut microbiome that are either enriched or depleted in PD.

Dataset

Fecal metagenomic sequencing data for PD patients and controls from the BioCollective

Fecal metagenomic sequencing data associated with Boktor et al., 2023. This dataset includes samples from the BioCollective cohort.

Dataset

Fecal metagenomic sequencing data for PD patients and controls from Rush University Medical Center

Fecal metagenomic sequencing data associated with Boktor et al. (2023). This dataset includes samples from the Rush University Medical Center cohort.

Code

Code for integrated multi-cohort analysis of the Parkinson’s disease gut metagenome

Detailed scripts to reproduce all analysis and data visualization for the paper, “Integrated multi-cohort analysis of the Parkinson’s disease gut metagenome,” including an interactive shiny R app for exploration of metagenomic features of interest in the data sets.

Article

Dopamine transporter and synaptic vesicle sorting defects initiate auxilin-linked Parkinson’s disease

Published: Auxilin helps in recycling of synaptic vesicles to facilitate neurotransmission and loss of auxilin is associated with PD. The authors show auxilin knockout mice exhibit typical PD pathology, dopamine transport is disrupted due to slower dopamine reuptake kinetics, and that macroautophagy and defective synaptic vesicle sorting contributes to dopamine dyshomeostasis. View original preprint.

Dataset

Peripheral neuronal activation of the intestinal tract shapes the microbiome and alters gut physiology-RNAseq

This RNA data set corresponds to the preprint: Neuronal Activation of the Gastrointestinal Tract Shapes the Gut Environment in Mice (Yoo et al., 2021).

Code

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

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.

 

Article

Gut microbiome-mediated regulation of neuroinflammation

Review: The intestinal microbiome influences neuroinflammatory disease in animal models, and recent studies have identified multiple pathways of communication between the gut and brain. As preclinical research findings and concepts are applied to humans, the potential impacts of the gut microbiome – brain axis on neuroinflammation represent exciting frontiers for further investigation.

 

Article

Interactions of dopamine, iron, and alpha-synuclein linked to dopaminergic neuron vulnerability in Parkinson’s disease and Neurodegeneration with Brain Iron Accumulation disorders

Review: This review analyzes the involvement of disrupted dopamine, alpha-synuclein, and iron pathways in dopamine neuron physiology and function, and discusses how disrupted interplay of dopamine, alpha-synuclein, and iron pathways may synergize to promote pathology and drive the unique vulnerability to disease states.

 

Protocol

Activation Induced Marker (AIM) Staining Protocol

This protocol details about activation induced marker staining.

Article

A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice

Publication: The gut microbiome is altered in PD and may impact motor and GI symptoms as indicated by animal studies, although mechanisms of gut-brain interactions remain incompletely defined. Here, the authors investigated whether a fiber-rich diet influences microglial function in α-synuclein overexpressing (ASO) mice, a preclinical model with PD-like symptoms and pathology. View original preprint.

 

Article

Border-associated macrophages mediate the neuroinflammatory response in an alpha-synuclein model of Parkinson disease

Preprint: The authors explored the role of resident macrophages in alpha-synuclein-mediated neuroinflammation. They found that border-associated macrophages (BAMs) play a key role in alpha-synuclein induced neuroinflammation where BAMs play a role in immune cell recruitment, infiltration, and antigen presentation.

Article

Subcellular and regional localization of mRNA translation in midbrain dopamine neurons

Published: Midbrain dopaminergic neurons have broad dendritic and axonal arborizations, but local protein synthesis is not understood here. Using, 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. View original preprint.

Dataset

Subcellular and regional localization of mRNA translation in midbrain dopamine neurons

This dataset is a part of “Subcellular and regional localization of mRNA translation in midbrain dopamine neurons” (Hobson et al., 2022) where the authors investigated mRNA localization in midbrain dopaminergic (mDA) neurons, cells with enormous axonal and dendritic projections, both of which can release dopamine (DA).