Protocol specific for LRRK2 Antibody (NB300-268)

Immunofluorescence Protocol:

1. Mouse CAD cells were transfected with Human wild-type LRRK-2.
2. 48hr following transfection, the cells were fixed for 10 min with ice-cold MeOH.
3. The cells were washed 3X with PBS, blocked with 10% normal donkey serum (NDS) in PBS containing 0.25% Triton for 1 hr at room temperature.
4. The cells were incubated overnight at 4C with rabbit anti-LRRK2 (Cat. # NB 300-268) diluted 1/2000 in 1% NDS in PBS containing 0.25% Triton.
5. The following day, the cells were washed 5X with PBS and incubated with FITC conjugated donkey anti-rabbit (1/100) diluted in 1% NDS in PBS containing 0.25% Triton for 1 hr.
6. The cells were washed 5X with PBS and mounted with Vectashield, and visualized with a 40X oil-immersion objective.

Protocol for immunoprecipitation of LRRK2 followed by LRRK2 autophosphorylation kinase assay

Cell lysis
3X15 cm plates of SH-SY5Y cells were grown to 80% confluency. The plates were washed twice with PBS and placed on ice. Remaining PBS was aspirated off after tilting plate to remove all PBS. 1.5 ml of cold lysis buffer (buffer A) was added to each plate. The plates were allowed to incubate on ice 5 min until the cells detached. The lysis buffer and cells for each plate were then vigorously passed 6X through a 30.5 guage needle. Lysis buffer and cells were transferred to 3X1.5 ml eppendorf tubes and spun 5 min. at 5,000 rpm in a 4 degree eppendorf microfuge. Lysates were removed from pelleted debris and transferred to new 1.5 ml eppendorf tubes and recentrifuged 10 min. at 13,000 rpm. Lysate was transferred to three new tubes and 1/2 lysate volume of buffer A (-) NaCl was added to each tube.
Preclear
10 ug of rabbit IgG were added to the lysate for each tube and the lysate was vortexed followed by rotating at 4 degrees for 2 hours. 20 ul of protein A sepharose beads (Amersham cat#: 17-0469-01) were added. The tubes were vortexed and then rotated for 1.5 hours at 4 degrees. Lysates were separated from protein A beads beads by low (200 rpm) spin for 2 min and transferred to new eppendorf tubes. A repeat of the protein A sepharose incubation was carried out to remove residual rabbit IgG followed by removal of the protein A beads.

Immunoprecipitation with LRRK2 Ab

To two of the tubes containing precleared lysate were added 7 ul of LRRK2 Ab (7ug). To the remaining tube was added 7ug of rabbit IgG. The tubes were vortexed and allowed to rotate overnight at 4 degrees. The following morning 30 ul of protein A sepharose was added to each tube, the tubes were vortexed and rotated at 4 degrees for 2 hours. The protein A beads were then isolated by brief, low speed centrifugation and were washed 3X in 500ul buffer A (-) NaCl. This was followed by two washes in kinase buffer (buffer B). Protein A beads were resuspended in 1 volume (30 ul) of buffer B for a total of 60ul of immunoprecipitate.
Autophosphorylation kinase reaction, gel electrophoresis and phosphoimaging
On ice, 40 ul of immunoprecipitate from each tube was transferred to a .5ml kinase reaction tube. Each of the three reactions was supplemented with a 5 ul mixture that gave a final reaction concentration of 15 uM cold ATP and 5uCi ATP. The reaction mixtures were vortexed and transferred to a rotator in a 30 degree incubator. The autophosphorylation incubation was allowed to go for 30 minutes and the reaction tubes were taken off the rotator and vortexed every five minutes. The reactions were then halted by addition of 11ul of 5X SDS gel running sample buffer to each of the three samples. 40ul of each sample was then run on a 7% acrylamide-acetate mini-gel. Once the 200Kd molecular weight marker band had run half way down the gel, the gel was stopped dried and exposed blanked to a phosphoimaging cassette (Molecular Dynamics). Following 24 hour exposure, the cassette was assessed for radioactivity on a Storm analyzer.

Buffers

Buffer A (make 10ml both - and + NaCl solutions) = lysis buffer
50mM Tris pH 7.4
150mM NaCl
0.2% NP40
Protease inhibitor cocktail (stock = 100X, Sigma)
0.5mM vanadate
15mM EDTA
adjust to 10 ml with H2O
Buffer B = kinase buffer
10mM hepes
10mM MgCl2
50mM NaCl
protease inhibitor
vanadate
(1mM NaN3 if storing overnight or longer)

IHC-FFPE sections
I. Deparaffinization:
A. Treat slides with Xylene: 3 changes for 5 minutes each. Drain slides for 10 seconds between changes.
B. Treat slides with 100% Reagent Alcohol: 3 changes for 5 minutes each. Drain slides for 10 seconds between changes.

II. Quench Endogenous Peroxidase:
A. Place slides in peroxidase quenching solution: 15-30 minutes.
To Prepare 200 ml of Quenching Solution:
Add 3 ml of 30% Hydrogen Peroxide to 200 ml of Methanol.
Use within 4 hours of preparation
B. Place slides in distilled water: 2 changes for 2 minutes each.

III. Retrieve Epitopes:
A. Preheat Citrate Buffer. Place 200 ml of Citrate Buffer Working Solution into container, cover and place into steamer. Heat to 90-96 degrees Celcius.
B. Place rack of slides into hot Citrate Buffer for 20 minutes. Cover.
C. Carefully remove container with slides from steamer and cool on bench, uncovered, for 20 minutes.
D. Slowly add distilled water to further cool for 5 minutes.
E. Rinse slides with distilled water. 2 changes for 2 minutes each.

IV. Immunostaining Procedure:
A. Remove each slide from rack and circle tissue section with a hydrophobic barrier pen (e.g. Liquid Blocker-Super Pap Pen).
B. Flood slide with Wash Solution. Do not allow tissue sections to dry for the rest of the procedure.
C. Drain wash solution and apply 4 drops of Blocking Reagent to each slide and incubate for 15 minutes.
D. Drain Blocking Reagent (do not wash off the Blocking Reagent), apply 200 ul of Primary Antibody solution to each slide, and incubate for 1 hour.
E. Wash slides with Wash Solution: 3 changes for 5 minutes each.
F. Drain wash solution, apply 4 drops of Secondary antibody to each slide and incubate for 1 hour.
G. Wash slides with Wash Solution: 3 changes for 5 minutes each.
H. Drain wash solution, apply 4 drops of DAB Substrate to each slide and develop for 5-10 minutes. Check development with microscope.
I. Wash slides with Wash Solution: 3 changes for 5 minutes each.
J. Drain wash solution, apply 4 drops of Hematoxylin to each slide and stain for 1-3 minutes. Increase time if darker counterstaining is desired.
K. Wash slides with Wash Solution: 2-3 changes for 2 minutes each.
L. Drain wash solution and apply 4 drops of Bluing Solution to each slide for 1-2 minutes.
M. Rinse slides in distilled water.
N. Soak slides in 70% reagent alcohol: 3 minutes with intermittent agitation.
O. Soak slides in 95% reagent alcohol: 2 changes for 3 minutes each with intermittent agitation.
P. Soak slides in 100% reagent alcohol: 3 changes for 3 minutes each with intermittent agitation. Drain slides for 10 seconds between each change.
Q. Soak slides in Xylene: 3 changes for 3 minutes each with intermittent agitation. Drain slides for 10 seconds between each change.
R. Apply 2-3 drops of non-aqueous mounting media to each slide and mount coverslip.
S. Lay slides on a flat surface to dry prior to viewing under microscope.

NOTES:
-Use treated slides (e.g. HistoBond) to assure adherence of FFPE sections to slide.
-Prior to deparaffinization, heat slides overnight in a 60 degrees Celcius oven.
-All steps in which Xylene is used should be performed in a fume hood.
-For Epitope Retrieval, a microwave or pressure cooker may be substituted for the steamer method. Adjust times as necessary depending on conditions.
-For the initial IHC run with a new primary antibody, test tissues with and without Epitope Retrieval. In some instances, Epitope Retrieval may not be necessary.
-200 ul is the recommended maximum volume to apply to a slide for full coverage. Using more than 200 ul may allow solutions to wick off the slide and create drying artifacts. For small tissue sections less than 200 ul may be used.
-5 minutes of development with DAB Substrate should be sufficient. Do not develop for more than 10 minutes. If 5 minutes of development causes background staining, further dilution of the primary antibody may be necessary.
-Hematoxylin should produce a light nuclear counterstain so as not to obscure the DAB staining. Counterstain for 1-1 1/2 minutes for nuclear antigens. Counterstain for 2-3 minutes for cytoplasmic and membranous antigens. If darker counterstaining is desired increase time (up to 10 minutes).