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11 protocols using ab1903

1

Immunocytochemistry of α-Synuclein and Pericytes

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At endpoints, cells were fixed in 4% paraformaldehyde for 15 min and washed/permeabilised with phosphate buffered saline (PBS) with 0.2% Triton X-100TM (PBS-T). Cells were incubated overnight at 4°C with primary antibodies—targeting α-syn (Mouse anti α-syn, AA 124–134, ab1903, Abcam; Mouse anti α-syn 4B12, AA 103–108, IgG1, MA1-90346, ThermoFisher; pericytes (Rabbit anti-PDGFR β, ab32570, Abcam; gt PDGFR β, AF-385, R&D systems)—diluted in immunobuffer (1% goat or donkey serum, 0.2% Triton X-100 in PBS). Cells were rewashed in PBS-T and incubated with filtered (0.22 μm syringe filter, Merck) fluorescently conjugated secondary antibodies and 20 μM Hoechst 33258 (ThermoFisher) for 2 hours at room temperature. Images were acquired using the automated fluorescence microscope ImageXpress® Micro XLS (Version 5.3.0.1, Molecular Devices) using the 20 x (0.45 NA) CFI Super Plan Fluor ELWD ADM objective lens and Lumencor Spectra X configurable light engine source. Confocal images were acquired using a LSM 800 Airyscan confocal microscope (Zeiss LSM 800 Airyscan confocal microscope) with a 40x/1.3 or 63x/1.4 NA Plan Apochromat oil immersion using the Airyscan module.
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2

Western Blot Analysis of Synuclein

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Protein was loaded on 4–12% Bis-Tris NuPAGE gels (ThermoFisher), separated by electrophoresis and transferred to Hybond PVDF membrane (GE Healthcare). For TX-100 soluble/insoluble studies, the amount of urea-SDS fraction loaded for each sample was calculated as a proportion of the protein concentration in the TX-100 soluble fraction. Because of the purity of the insoluble fraction neither β-actin nor GAPDH were detectable in the insoluble fraction. For α-syn blots, PVDF was fixed with 4% paraformaldehyde and 0.01% (v/v) glutaraldehyde for 30 min at room temperature (62 (link)). Membranes were blocked with 5% milk/PBS/0.1% (v/v) Tween 20 and incubated with the following primary antibodies: α-syn (abcam, ab1903 for mouse; ab80627 for human), α-syn phospho S129 (abcam, ab51253), β-actin (abcam, ab6276), GAPDH, (abcam, ab8245), GCase (Merck, 2E2 for human; Sigma, G4171 for mouse), GRP78/BiP (abcam, ab21685), HA (Biolegend, HA.11), histone H3 (abcam, ab1791), LIMP2 (abcam, ab16522), TFEB (abcam, ab2636), TH (abcam, ab112). Following incubation with respective HRP-conjugated secondary antibodies, blots were incubated with Immobilon Luminata Forte enhanced chemiluminescence (Merck) and images acquired and quantified using Image Lab software (BioRad). Band densities were normalized to β-actin or GAPDH.
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3

Immunofluorescent Staining of HEK-293T Neurons

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HEK-293T neurons growing on glass coverslips were fixed in 4% paraformaldehyde for 15 min and then washed twice with PBS containing 20 mM glycine before permeabilization with the same buffer containing 0.2% Triton X-100 (5 min incubation). Cells were treated for 1 h with PBS containing 1% bovine serum albumin. To detect the expression of NR1-Rluc, cells were labeled with a mouse anti-Rluc antibody (1/100; MAB4400, Millipore, Burlington, MA, USA) and subsequently treated with Cy3-conjugated anti-mouse IgG secondary antibody (1/200; 715-166-150; Jackson ImmunoResearch, West Grove, PA, USA) (1 h each). The expression of CB1R-YFP was detected by the YFP’s own fluorescence. The presence of α-syn fibrils was detected with a mouse monoclonal anti-human α-synuclein antibody (1/300; ab1903, Abcam). Phalloidin was detected with an AF488 pre-stained anti-phalloidin probe (1/200; A12379, ThermoFisher, Waltham, MA, USA). Nuclei were stained with Hoechst33432 (1/100 from stock 1 mg/mL; Thermo Fisher, Waltham, MA, USA). The samples were washed several times and mounted on glass slides with ShandonTM Immu-MountTM (9990402; ThermoFisher, Waltham, MA, USA). Samples were observed under a Zeiss 880 confocal microscope (Carl Zeiss, Oberkochen, Germany) equipped with an apochromatic 63× oil-immersion objective (N.A. 1.4) and with 405 nm, 488 nm, and 561 nm laser lines.
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4

Proximity Ligation Assay for α-Synuclein Interactions

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A proximity ligation assay (PLA) was performed according to the manufacturer’s instructions using Duolink kit supplied by Sigma (Sigma-Aldrich Company Ltd, Gillingham, UK). Four tissue sections from MSA cases were examined for PLA. Two were utilised as negative controls without primary antibodies. Mouse anti-α-synuclein (Abcam ab1903, 1:1,000) and rabbit anti-MOBP (Atlas Antibodies HPA035152, 1:200) or anti-HIP1 (Abcam ab181238, 1:100) antibodies were used as primary antibodies for PLA. As reported previously (20 (link)), anti-α-synuclein and MOBP or HIP1 antibodies were applied to the samples and incubated for 1h at room temperature. PLA probes (Minus and Plus) detecting each antibody were added to the samples for 1h at 37°C. PLA probe hybridization and ligation was performed using ligation solution for 30 min at 37°C. Polymerase solution was then added to the samples for 120 min at 37°C. The samples were mounted and examined using a light microscope.
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5

Quantitative Dot-Blot Analysis of α-Synuclein

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For dot-blotting [26 (link)], lysates (1 μg per dot) were spotted onto polyvinylidene difluoride membrane using a narrow-mouth pipette tip and air-dried. After blocking in 5% bovine serum albumin in tris-buffered saline with Tween 20 for 1 h at room temperature, the blot was incubated with a mouse monoclonal antibody against total SNCA (4D6, 1 : 5000) (ab1903; Abcam, Cambridge, UK). After subsequent washes, the blot was incubated with 1 : 2000 anti-rabbit horseradish peroxidase- (HRP-) conjugated secondary antibody (goat anti-mouse immunoglobulin/HRP) and then developed with enhanced chemiluminescence reagent. The relative amount of α-syn in samples was quantified by Gel-Pro analyzer software (Rockville, MD, USA).
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6

Proximity Ligation Assay for α-Synuclein

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Cells in suspension were incubated with vehicle or α-syn PFFs (1 μM) on ice for 30 min to allow binding, but not internalization, of α-syn PFFs. Unbound α-syn PFFs were washed away, and cells were fixed in 2% formaldehyde solution on ice for 30 min. A proximity ligation assay (PLA) was performed using a Duolink® FlowPLA kit following the manufacturer’s recommendations. The following primary antibodies were used: rabbit anti-α-syn (1:200; ab138501, Abcam), mouse anti-α-syn (1:200; ab1903, Abcam), mouse anti-MerTK (1:1000; 367602, Biolegend) and mouse anti-AXL (1:1000; MAB154, R&D Systems). Antibodies against α-syn were tested on vehicle versus α-syn PFF-treated cells to ensure that they selectively bound to exogenous but not endogenous α-syn (Supplementary Fig. 3). Data acquisition was done on an AttuneTM Nxt Flow Cytometer and analysis was done using FlowJoTM software.
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7

Protein-Protein Interaction Analysis in Multiple System Atrophy

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A PLA was performed according to the manufacturer's instructions using Duolink kit supplied by Sigma (Sigma‐Aldrich Company Ltd). Four tissue sections from MSA cases were examined for PLA. Two were utilized as negative controls without primary antibodies. Mouse anti‐SNCA (Abcam ab1903, 1:1000) and rabbit anti‐MOBP (Atlas Antibodies HPA035152, 1:200) or anti‐HIP1 (Abcam ab181238, 1:100) antibodies were used as primary antibodies for PLA. As reported previously,20 (link) anti‐SNCA and MOBP or HIP1 antibodies were applied to the samples and incubated for 1h at room temperature. PLA probes (Minus and Plus) detecting each antibody were added to the samples for 1 h at 37°C. PLA probe hybridization and ligation was performed using ligation solution for 30 min at 37°C. Polymerase solution was then added to the samples for 120 min at 37°C. The samples were mounted and examined using a light microscope.
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8

Western Blot Analysis of α-Synuclein Phosphorylation

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The samples were heated at 95°C for 5 min, loaded on 12% polyacrylamide gels, and subjected to SDS-PAGE. After electrophoresis, the proteins were transferred to a nitrocellulose membrane. The membrane was fixed with 4% PFA and 0.01% glutaraldehyde in PBS for 30 min to retain α-synuclein.60 (link) After fixation, the membrane was washed 3 × 5 min in TBS. The membrane was then blocked in 3% milk in TBS-T (0.01% Tween-20 in TBS) for 60 min and then incubated with primary antibody (in TBS-T with 3% skim milk) overnight at 4°C. Next day, the membrane was washed 3 × 15 min in TBS-T, incubated with secondary antibody (in TBS-T with 3% skim milk) for 1 h at RT, and then washed 3 × 15 min with TBS-T and once for 15 min with TBS. The secondary antibodies used were IRDye from LI-COR Biosciences (Lincoln, NE, USA) at 1:10,000 dilution. The membranes were scanned on an Odyssey CLx imaging system from LI-COR Biosciences, and the band intensities were analyzed from the images using the Odyssey CLx software. Antibody used to detect total α-synuclein was the ab1903 (Abcam) and for detection of the pSer129 α-synuclein, the ab51253 (Abcam).
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9

Immunohistochemical Analysis of SNCA Oligomers in Hippocampus

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Mice were perfused with cold phosphate-buffered saline (PBS) followed by 4% paraformaldehyde (PFA) under anesthesia. The brain was removed and fixed in 4% PFA at 4°C overnight, according to a previous protocol [26 (link)]. After dehydration, clearing, paraffin infiltration, and embedding, the whole hippocampus was sectioned into sections of 6 μm thickness. After antigen retrieval, paraffin tissue sections were blocked using goat serum for 30 min at room temperature. Accumulation of SNCA oligomers was detected by immunohistochemistry using a rabbit polyclonal SNCA oligomer-specific Syn33 antibody (ABN2265; Merck Millipore, Billerica, MA, USA), a mouse monoclonal antibody against total SNCA (4D6, ab1903; Abcam), a rabbit polyclonal COXIV antibody (11242-1-AP; Proteintech), a rabbit monoclonal antibody against p-α-syn (Ser129, ab1903; Abcam), and a rabbit monoclonal antibody against Iba-1 (Wako 019-19741; Rosemont, IL, USA). Subsequent incubation was performed using goat anti-rabbit/mouse Alexa Fluor® 594 (ab150116 and ab150080; Abcam) and goat anti-rabbit Alexa Fluor® 488 secondary (ab150077; Abcam) antibodies.
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10

Immunohistochemical Analysis of Protein Aggregation

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Imunohistochemical analysis of protein aggregation was evaluated in three slices/region/animal, with a total of 15 slices/region/animal taken, between Bregma levels from -3.6 mm to -4.1 mm for the hippocampus, -5.5 mm to -5.8 mm for the substantia nigra and -9.6 to -10.0 for the locus coeruleus. The whole hippocampus, substantia nigra and locus coeruleus were analyzed, without any distinction of the subarea (hippocampus: CA/dentate gyrus; substantia nigra: pars compacta/pars reticulata)
Sections were incubated for 24 hours at 4°C with antibodies against either hyperphosphorylated TAU 1/200 (Santa Cruz Biotechnology, sc-101813), alpha-synuclein 1/200 (Abcam, ab1903) or amyloid-beta peptide 1/200 (Abcam, ab14220), followed by incubation with biotinylated secondary goat anti-rabbit immunoglobulin antibodies (1/230, Vector, USA) for 90 min. Sections were then incubated with avidin-biotin peroxidase complex (1:120, Vectastain, Vector, USA) for 45 minutes and immunoreactivity was visualized using 3-3'-diaminobenzidine tetrahydrochloride (DAB, Sigma) as chromogen and H 2 O 2 (0.05%) for six minutes of reaction. Cells were counterstained with hematoxylin, which is a valuable tool to stain nuclei. The use of hematoxylin facilitates intracellular localization of protein aggregates.
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