Output 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 created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.
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Output Type
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Program
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CRN Team Name
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Theme
HyDrop Bead Generation & PCR Barcoding V.2
Protocol for producing dissolvable barcoded hydrogel beads used in HyDrop experiments.
Structural remodeling of the mitochondrial protein biogenesis machinery under proteostatic stress
Cryo-ET showed protein aggregates, altered cristae, and reduced ribosome complexes in stressed mitochondria. Mitochondrial Hsp60 undergoes conformational changes to aid in protein folding, shedding light on mitochondrial proteostasis mechanisms.
ATP13A4 gates extracellular polyamine levels to control excitatory synaptogenesis
Polyamines are crucial for brain function. ATP13A4 is the main polyamine transporter in astrocytes, impacting astrocyte morphology, synapse formation, and neurodevelopment. Mutations in ATP13A4 are linked to neurodevelopmental disorders.
Ancestry-specific peripheral immune gene-expression mediates the risk of neurodegenerative disease
This study shows that genes linked to brain diseases like Alzheimer’s and Parkinson’s act through the immune system outside the brain, with effects varying by ancestry. It highlights the need for ancestry-specific genetic studies.
Single cell eQTL mapping reveals convergent glial–neuronal risk architecture in Parkinson’s disease
Population-scale, disease-context aware meta single-nucleus eQTLs mapping (N = 1,197) in nine cell types from cortex and substantia nigra identifies 125 risk genes and cell types for PD GWAS signals.
An ImageJ/FIJI Preprocessing Workflow for Multi-Series Confocal Microscopy Datasets Prior To CellProfiler Analysis
A workflow using ImageJ/FIJI aims to create three-slice MIPs from multi-series .czi files to capture weak signals. It involves extracting datasets, creating projections, and saving images for efficient analysis in CellProfiler.
Health phenome of Parkinson’s patients reveals prominent mood-sleep cluster
In 933 PD cases vs 291 controls, mood/sleep disorders (depression, anxiety, apnea, RLS) were more common and clustered. Pesticides and head trauma raised odds; smoking lowered. 43% of PD had a mood/sleep disorder.
Methods for “Cholesterol Dysregulation in APOE4 Astrocytes Promotes α-Synuclein Pathology in miBrains, a Human Brain Tissue Model”
Collection of protocols used for the manuscript entitled "Cholesterol Dysregulation in APOE4 Astrocytes Promotes α-Synuclein Pathology in miBrains, a Human Brain Tissue Model".
Raw datasets for “Cholesterol Dysregulation in APOE4 Astrocytes Promotes α-Synuclein Pathology in miBrains, a Human Brain Tissue Model”
This dataset contains all primary data and quantifications
CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species
CREsted, a sequence-based deep learning model, analyzes genomic regulatory code, decodes enhancer grammar, and designs synthetic enhancers. It preprocesses single-cell data, models chromatin accessibility, and compares cell states across tissues.
A druggable ATP13A3–antizyme switch controls adaptive polyamine uptake in cancer
Cellular polyamine depletion for cancer treatment is hindered by compensatory uptake. ATP13A3, not ATP13A2, is the key polyamine importer affected by DFMO. Antizyme inhibits uptake by ATP13A3, suggesting a targetable strategy for cancer therapy.
Cryo-EM structure of soluble VPS13C suggests its regulation by a conformational switch and by calmodulin
Structural studies of the Parkinson's protein VPS13C provide a molecular basis for understanding its function and regulation.
Q-DOAS: A Proximity Quenching Assay for Real-Time Detection of Early Protein Aggregation Events
We describe Q-DOAS, a plate-reader assay that quantifies protein self-assembly in real time via proximity-quenching of a single, site-specifically conjugated dye (BODIPY-TMR), and which allows quantification of pre-amyloid oligomers.
Culturing, transfection and NBD-labeled lipid uptake assay in HeLa-CDC50A-OE cells
Assay for NBD-labeled lipid uptake in HeLa-CDC50A-OE cells includes seeding, transfection, and flow cytometry to measure flippase construct activity, enabling quantitative assessment of lipid uptake.
Flow cytometry data from the manuscript “Fluorescence-Gated Flow Cytometry Approach for Measuring Lipid Flippase Activity in Mamma-lian Cells”
Summary: The manuscript presents a fluorescence-gated flow cytometry method to measure lipid flippase activity in mammalian cells.
