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7 protocols using lrrk2 in 1

1

Protein Detection: Antibodies and Reagents

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A summary of the primary antibodies used in this study can be found in SI Appendix, Table S1. The following secondary antibodies conjugated to horseradish peroxidase were used for immunoblotting: RRID:AB_2099233, RRID:AB_330924, and RRID:AB_228395. Immunofluorescence experiments used the following secondary antibodies: RRID:AB_2535794 and RRID:AB_141637. The following chemicals were used: Y-27632 Rock inhibitor (Tocris Bioscience), MLi-2 (Abcam #254528), LRRK2-IN-1 (Tocris Bioscience # 4273), and EDTA (Invitrogen #15575-038).
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2

Mitophagy and Neurodegeneration Protocol

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DMEM-F12 (Dulbecco's modified Eagle's medium), penicillin–streptomycin, gentamicin and fetal bovine serum (FBS) were purchased from Gibco-Invitrogen (Carlsbad, CA, USA). GSK 2578215A and LRRK2-IN-1 were purchased from Tocris Bioscience (Minneapolis, MN, USA). Stealth RNAi duplexes were purchased from Life Technologies (Carlsbad, CA, USA). BCA protein assay was from Pierce (Rockford, IL, USA). The pDsRed2-mito vector was provided by Clontech (BD Biosciences, San Jose, CA, USA), GFP-LC3 was provided by Dr. JM Fuentes (Universidad de Extremadura, Badajoz, Spain), Drp1-GFP was provided by T Wilson and Dr. S Strack (Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA, USA) and mRFP-GFP-LC3 was provided by Dr. E Kneck (Laboratory of Cellular Biology, Centro de Investigación Príncipe Felipe, Valencia, Spain). Anti-4 hydroxynonenal and LRRK2 antibodies were purchased from Abcam (Cambridge, UK); anti-p62 from BD (San Jose, CA, USA) and Alexa Fluor 488 were from Molecular Probes (Carlsbad, CA, USA), Invitrogen (Carlsbad, CA, USA); and anti-acetylated tubulin was from Sigma-Aldrich (St. Louis, MO, USA). The TUNEL method (MEBSTAIN Apoptosis Kit) was purchased from MBL (Carlsbad, CA, USA). Mdivi-1 was purchased from Sigma-Aldrich.
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3

Inhibitors of Microtubule Dynamics

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Trichostatin A, tubacin and nocodazole were from Sigma Aldrich, PTL from Eurodiagnostico, LRRK2-IN1, TAE684 and CZC25146 from the Michael J. Fox Foundation, GSK2578215A from Tocris, compound 68 (ID 9108605) and compound 70 (ID 9119202) from Chembridge Corporation (San Diego, USA), and GNE-0877 and GNE-7915 from MedchemExpress (USA), and MLi2 from MRC PPU, Dundee, UK. Natural streptolysin-O was from Abcam (ab63978), and non-hydrolyzable GTP test kit from Jena Bioscience (NK-102).
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4

LRRK2 inhibitor-mediated autophagy regulation

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Chemical compounds were purchased as follows: LRRK2in1 [24 (link)] from the Division of Signal Transduction Therapy, School of Life Sciences, University of Dundee, U.K.; GSK2578215A and MLi-2 from Tocris [25 (link)]; bafilomycin-A1 (B1793-2UG) and cycloheximide (01810-1G) from Sigma-Aldrich; torin-1 (CAY10997) from Cayman Chemicals. Antibodies used were as follows: LC3 (NB100-2220, Novus Biologicals); total P70S6K (sc-8418, Santa Cruz); phospho Thr389 P70S6K (sc-11759, Santa Cruz); p62 (610833, BD Transduction Labs); total ULK1 antibody (8054 and 4773, Cell Signalling); phospho Ser757 ULK1 antibody (6888 and D7O6UCell Signalling); phospho Ser555 ULK1 antibody (5869, Cell Signalling); total LRRK2 antibody (MJFF2, Abcam); phosphor Ser935 LRRK2 antibody (UDD2, Abcam) and β-actin (A1978, Sigma-Aldrich). AMPK activator (A769662) was kindly provided by Dr MPMS.
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5

Stimulating Cell Responses with Diverse Agents

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Where indicated, cells were treated with recombinant human IFN-γ (R&D Systems), LPS (LPS from E. coli O111:B4), poly(I:C) (both Invivogen), ionomycin, MG132, colchicine, PMA (all from Sigma-Aldrich), LRRK2-IN-1 and GSK2578215A (both Tocris), Mli-2 (Abcam), MCV1 (HPVIVIT, Calbiochem), recombinant human NRG1 (BioLegend), and PTX (STEMCELL Technologies).
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6

Preparation of Primary Neuronal Cultures

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Primary neuronal cultures from cortex, striatum and hippocampus from pups at P0 were prepared as described previously55 (link). In brief, neurons were dissociated by papain buffer (Sigma Aldrich), and were then placed in poly-D-lysine slides (BD) or plates in Basal Eagle Medium (Sigma-Aldrich). Arabinosylcytosine (Sigma-Aldrich) was used to inhibit glial cell growth. Forskolin (FSK), PKI (PKA inhibitor) and LRRK2 kinase inhibitor LRRK2-IN-1 (Tocris Bioscience, Bristol, UK) as well as all the other compounds were added directly to the medium of cortical neurons from stock solution and unless otherwise stated these compounds were from Calbiochem.
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7

Kinase Inhibitor Screening Protocol

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Cobalt(II) chloride hexahydrate (CoCl2), L-Glutamic acid monosodium salt hydrate, hydrogen peroxide (H2O2), and 2-Methoxyestradiol (2ME2) were purchased from Sigma-Aldrich. GSK2578215A (#4629) and LRRK2-IN-1 (#4273) were obtained from Tocris Bioscience. G1023, MLi-2, and PF-06447475 were synthesized by Dr. Hwan Geun Choi at Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF, Daegu, South Korea). Information about antibodies used in this study is provided in Supplementary Table 2.
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