We thank the healthy volunteers who kindly donated blood for the present study. We thank The Michael J. Fox Foundation for Parkinson&#8217;s Research (MJFF) and the Fox BioNet study leadership (FBN) for their support and input towards the written protocol and the video. We thank Professor Alexander Zimprich from the University of Vienna in Austria for testing our protocol and collaboration. We value the contributions of Paul Davies to the project (general manager of the MRC PPU). We also recognize the excellent technical support of the MRC Protein Phosphorylation and Ubiquitylation Unit (PPU) namely Chemical Synthesis (Natalia Shpiro for synthesising MLi-2), MRC PPU Reagents and Services antibody purification teams (coordinated by Hilary McLauchlan and James Hastie). We thank Mhairi Towler and Fraser Murdoch from Vivomotion for their help with making the videos and animations. We thank Steve Soave from 81 films for assistance with the final edits. Esther Sammler is supported by a Scottish Senior Clinical Academic Fellowship and has received funding from Parkinson&#39;s UK (K-1706).

According to local UK regulation all manipulations and pipetting of human blood are undertaken in a category 2 biological safety cabinet. All procedures were performed in compliance with local ethics review board and all participants have provided informed consent.
1. Preparation
<ol>
	<li>Prepare 0.1 mL of EDTA Stock Solution 1 containing 100 mM EDTA in phosphate-buffered saline (PBS).</li>
	<li>Prepare 60 mL of EDTA Stock Solution 2 containing 1 mM EDTA in PBS.</li>
	<li>Prepare lysis buffer containing 50 mM Tris-HCl (pH = 7.5), 1% (v/v) Triton X-100, 1 mM EGTA, 1 mM Na3VO4, 50 mM NaF, 10 mM &#946;-glycerophosphate, 5 mM sodium pyrophosphate, 0.27 M sucrose, 0.1% (v/v) &#946;-mercaptoethanol, 1x protease inhibitor cocktail, 1 &#956;g/mL microcystin-LR, and 0.5 mM diisopropyl fluorophosphate (DIFP). 
	NOTE: The authors routinely use an EDTA-free product, but an EDTA-containing protease inhibitor cocktail should also work. The lysis buffer can be made in advance without the &#946;-mercaptoethanol, protease inhibitors, microcystin-LR, and DIFP, and stored at 4 &#176;C until use. Ensure that the &#946;-mercaptoethanol, protease inhibitors, microcystin-LR, and DIFP is only added immediately before use. 
	CAUTION: DIFP is toxic and should be handled with care in a fume hood following local health and safety risk assessment. DIFP can be added to the lysis buffer and used immediately. Alternatively, the complete lysis buffer containing all other components, including DIFP, can be aliquoted and stored at -80 &#176;C for subsequent use for at least 4 weeks.</li>
</ol>
2. Neutrophil isolation from whole blood
<ol>
	<li>Collect 10 mL of blood into a blood collection tube. Mix gently by inverting tubes 7&#8722;8x.</li>
	<li>Transfer 10 mL of blood into a 50 mL conical tube.</li>
	<li>Add 100 &#956;L of EDTA Stock Solution 1 to the blood. Mix gently.</li>
	<li>Add 500 &#956;L of the isolation cocktail (50 &#956;L/mL) from the neutrophil isolation kit (Table of Materials) to the whole blood sample.</li>
	<li>Vortex the magnetic beads from the neutrophil isolation kit for 30 s before use in order to resuspend the very fine magnetic beads.</li>
	<li>Add 500 &#956;L of the magnetic beads to the blood sample and mix gently by inverting the tube several times.</li>
	<li>Incubate at room temperature (RT) for 5 min.</li>
	<li>Fill the tube to 50 mL with EDTA Stock Solution 2. Mix by very gently pipetting up and down 2&#8211;3x.</li>
	<li>Place the tube into the magnet and remove the lid to avoid subsequent agitation of the tube.</li>
	<li>Incubate for 10 min at RT.</li>
	<li>Carefully pipette the enriched cell suspension that contains the neutrophils into a new 50 mL conical tube. 
	NOTE: Do not touch the side of the tube that is in contact with the magnet and avoid collection and perturbation of the red blood cells at the bottom of the tube. Leave approximately 10 mL of the red blood cell suspension behind at the bottom of the tube.</li>
	<li>Vortex the magnetic beads for 30 s before use and add 0.5 mL of the magnetic beads to the tube containing the enriched neutrophils. Mix gently by inverting the tube.</li>
	<li>Incubate at RT for 5 min.</li>
	<li>Place the tube into the magnet and remove the lid to avoid subsequent agitation.</li>
	<li>Incubate at RT for 5 min.</li>
	<li>Carefully pipette the enriched cell suspension that contains the neutrophils into a new 50 mL conical tube. 
	NOTE: Do not touch the side of the tube that is in contact with the magnet. Leave approximately 5 mL of the suspension at the bottom of the tube.</li>
	<li>To ensure the complete removal of magnetic beads from the cell mixture, place the tube containing the enriched cells into the magnet.</li>
	<li>Incubate for 10 min at RT.</li>
	<li>Carefully pipette the enriched cell suspension that now contains pure neutrophils into a new 50 mL conical tube. 
	NOTE: Do not touch the side of the tube that is in contact with the magnet. Leave approximately 5 mL of the suspension at the bottom of the tube.</li>
	<li>Mix the isolated cells with 1 mM EDTA Stock Solution 2 to a final volume of approximately 41 mL. Pipette up and down to mix.</li>
	<li>Divide the solution equally into two tubes with approximately 20 mL in each tube.</li>
	<li>Centrifuge both tubes at 335 x g for 5 min.</li>
	<li>During this centrifugation take MLi-2 inhibitor stock (200 &#181;M/1,000x concentration) out of the -80 &#176;C freezer and leave at RT for subsequent use.</li>
	<li>Immediately after the centrifugation step and without agitation of the tubes, pour off the supernatant without disturbing the neutrophil pellets. Resuspend each cell pellet in 10 mL of cell culture media (Table of Materials) at RT by gently pipetting cells up and down 4x.</li>
</ol>
3. LRRK2 kinase inhibitor treatment of pure neutrophils
<ol>
	<li>Label one tube &#34;DMSO&#34; and the other tube &#34;MLi-2&#34;.</li>
	<li>To the &#34;DMSO&#34; labeled tube, add 10 &#181;L of DMSO and mix gently by pipetting up and down 2x with a 10 mL pipette. To the &#34;MLi-2&#34; labeled tube, add 10 &#956;L of 200 &#956;M MLi-2 stock solution (final concentration 200 nM) and mix gently by pipetting up and down 2x with a 10 mL pipette.</li>
	<li>Incubate the samples for 30 min at RT. Mix gently by inversion every 10 min during the incubation.</li>
	<li>During the incubation period, remove 0.5 M DIFP stock from the -80 &#176;C freezer and place in a fume hood on ice. Remove 1 mg/mL microcystin-LR stock solution from the -80 &#176;C freezer and leave at RT to thaw. Take an aliquot (0.25 mL) of the lysis buffer out of the freezer, allow it to defrost at RT, and then place it on ice for subsequent use.</li>
	<li>Prepare 1 mL of cell culture medium containing 1 &#956;L of DMSO and call this DMSO resuspension buffer. Prepare 1 mL of RPMI media containing 1 &#956;L of 200 &#956;M MLi-2 and call this MLi-2 resuspension buffer.</li>
	<li>After the 30 min incubation period, centrifuge both tubes at 335 x g for 5 min.</li>
	<li>Carefully discard the supernatant in each tube without disturbing the neutrophil pellet.</li>
	<li>For the DMSO labeled sample gently resuspend the pellet in 1 mL of the DMSO resuspension buffer and for the MLi-2 labeled tube, resuspend the pellet in 1 mL of the MLi-2 resuspension buffer.</li>
	<li>Transfer the resuspended cell pellets to corresponding centrifugation tubes labeled &#34;DMSO&#34; and &#34;MLi-2&#34; and centrifuge both tubes at 335 x g for 3 min.</li>
	<li>During the centrifugation step, prepare the lysis buffer. In the fume hood carefully add 0.25 &#956;L of 0.5 M DIFP solution as well as 0.25 &#956;L of 1 mg/mL microcystin-LR to the 0.25 mL lysis buffer. Mix and leave on ice until use. 
	NOTE: Add DIFP to the lysis buffer within 15 min of cell lysis, because DIFP is relatively unstable in an aqueous solution.</li>
	<li>Immediately after the centrifugation, carefully and completely remove all the supernatant with a pipette without disturbing the neutrophil pellet and place the tubes on ice.</li>
	<li>Immediately add 100 &#181;L of lysis buffer containing DIFP and microcystine-LR to each tube. Using a 100&#8211;200 &#956;L pipette, resuspend the cell pellets by pipetting up and down about 5&#8211;10x.</li>
	<li>Lyse the cells on ice for 10 min.</li>
	<li>Centrifuge tubes at 20,000 x g for 15 min at 4 &#176;C to remove cell debris.</li>
	<li>Transfer the &#34;DMSO&#34; and &#34;MLi-2&#34; supernatants containing the neutrophil lysates into new centrifugation tubes. Discard the debris pellet. 
	NOTE: The neutrophil lysates are now ready for use or can be snap frozen in liquid nitrogen and stored at -80 &#176;C for future analysis.</li>
</ol>

<ol>
	<li>Paisan-Ruiz, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cloning+of+the+gene+containing+mutations+that+cause+PARK8-linked+Parkinson's+disease.">Cloning of the gene containing mutations that cause PARK8-linked Parkinson's disease.</a> Neuron. 44 (4), 595-600 (2004).</li><li>Fell, M. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MLi-2,+a+Potent,+Selective,+and+Centrally+Active+Compound+for+Exploring+the+Therapeutic+Potential+and+Safety+of+LRRK2+Kinase+Inhibition.">MLi-2, a Potent, Selective, and Centrally Active Compound for Exploring the Therapeutic Potential and Safety of LRRK2 Kinase Inhibition.</a> Journal of Pharmacology and Experimental Therapeutics. 355 (3), 397-409 (2015).</li><li>Zimprich, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mutations+in+LRRK2+cause+autosomal-dominant+parkinsonism+with+pleomorphic+pathology.">Mutations in LRRK2 cause autosomal-dominant parkinsonism with pleomorphic pathology.</a> Neuron. 44 (4), 601-607 (2004).</li><li>Sardi, S. P., Cedarbaum, J. M., Brundin, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeted+Therapies+for+Parkinson's+Disease:+From+Genetics+to+the+Clinic.">Targeted Therapies for Parkinson's Disease: From Genetics to the Clinic.</a> Journal of Movement Disorders. 33 (5), 684-696 (2018).</li><li>Steger, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phosphoproteomics+reveals+that+Parkinson's+disease+kinase+LRRK2+regulates+a+subset+of+Rab+GTPases.">Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases.</a> Elife. 5, (2016).</li><li>Ito, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phos-tag+analysis+of+Rab10+phosphorylation+by+LRRK2:+a+powerful+assay+for+assessing+kinase+function+and+inhibitors.">Phos-tag analysis of Rab10 phosphorylation by LRRK2: a powerful assay for assessing kinase function and inhibitors.</a> Biochemical Journal. 473 (17), 2671-2685 (2016).</li><li>Alessi, D. R., SammLer, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=LRRK2+kinase+in+Parkinson's+disease.">LRRK2 kinase in Parkinson's disease.</a> Science. 360 (6384), 36-37 (2018).</li><li>Yue, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Progressive+dopaminergic+alterations+and+mitochondrial+abnormalities+in+LRRK2+G2019S+knock-in+mice.">Progressive dopaminergic alterations and mitochondrial abnormalities in LRRK2 G2019S knock-in mice.</a> Neurobiology of Disease. 78, 172-195 (2015).</li><li>Doggett, E. A., Zhao, J., Mork, C. N., Hu, D., Nichols, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phosphorylation+of+LRRK2+serines+955+and+973+is+disrupted+by+Parkinson's+disease+mutations+and+LRRK2+pharmacological+inhibition.">Phosphorylation of LRRK2 serines 955 and 973 is disrupted by Parkinson's disease mutations and LRRK2 pharmacological inhibition.</a> Journal of Neurochemistry. 120 (1), 37-45 (2012).</li><li>Sheng, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ser1292+autophosphorylation+is+an+indicator+of+LRRK2+kinase+activity+and+contributes+to+the+cellular+effects+of+PD+mutations.">Ser1292 autophosphorylation is an indicator of LRRK2 kinase activity and contributes to the cellular effects of PD mutations.</a> Science Translational Medicine. 4 (164), (2012).</li><li>Fan, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interrogating+Parkinson's+disease+LRRK2+kinase+pathway+activity+by+assessing+Rab10+phosphorylation+in+human+neutrophils.">Interrogating Parkinson's disease LRRK2 kinase pathway activity by assessing Rab10 phosphorylation in human neutrophils.</a> Biochemical Journal. 475 (1), 23-44 (2018).</li><li>Scott, J. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Discovery+of+a+3-(4-Pyrimidinyl)+Indazole+(MLi-2),+an+Orally+Available+and+Selective+Leucine-Rich+Repeat+Kinase+2+(LRRK2)+Inhibitor+that+Reduces+Brain+Kinase+Activity.">Discovery of a 3-(4-Pyrimidinyl) Indazole (MLi-2), an Orally Available and Selective Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitor that Reduces Brain Kinase Activity.</a> Journal of Medicinal Chemistry. 60 (7), 2983-2992 (2017).</li><li>Pham, C. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neutrophil+serine+proteases:+specific+regulators+of+inflammation.">Neutrophil serine proteases: specific regulators of inflammation.</a> Nature Reviews Immunology. 6 (7), 541-550 (2006).</li><li>Lis, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+phospho-specific+Rab+protein+antibodies+to+monitor+in+vivo+activity+of+the+LRRK2+Parkinson's+disease+kinase.">Development of phospho-specific Rab protein antibodies to monitor in vivo activity of the LRRK2 Parkinson's disease kinase.</a> Biochemical Journal. 475 (1), 1-22 (2018).</li><li>Mir, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Parkinson's+disease+VPS35[D620N]+mutation+enhances+LRRK2-mediated+Rab+protein+phosphorylation+in+mouse+and+human.">The Parkinson's disease VPS35[D620N] mutation enhances LRRK2-mediated Rab protein phosphorylation in mouse and human.</a> Biochemical Journal. 475 (11), 1861-1883 (2018).</li><li>Rieckmann, J. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Social+network+architecture+of+human+immune+cells+unveiled+by+quantitative+proteomics.">Social network architecture of human immune cells unveiled by quantitative proteomics.</a> Nature Immunology. 18 (5), 583-593 (2017).</li><li>Borregaard, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neutrophils,+from+marrow+to+microbes.">Neutrophils, from marrow to microbes.</a> Immunity. 33 (5), 657-670 (2010).</li><li>Bain, B., Dean, A., Broom, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+estimation+of+the+lymphocyte+percentage+by+the+Coulter+Counter+Model+S+Plus+III.">The estimation of the lymphocyte percentage by the Coulter Counter Model S Plus III.</a> Clinical &amp; Laboratory Haematology. 6 (3), 273-285 (1984).</li><li>Tomazella, G. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomic+analysis+of+total+cellular+proteins+of+human+neutrophils.">Proteomic analysis of total cellular proteins of human neutrophils.</a> Proteome Science. 7, 32 (2009).</li></ol>

The authors have nothing to disclose.

Compelling clinical, genetic, and biochemical evidence points towards an important role for LRRK2 and in particular its kinase function in Parkinson&#8217;s disease7. LRRK2 kinase inhibitors have been developed and are entering clinical trials2,4,12. As such there is a need for exploiting LRRK2 as a biomarker for target engagement as well as patient stratification. Our protocol describes a robust and easy...

Attempts to slow or stop Parkinson&#8217;s disease (PD) have thus far failed. The discovery of hyperactivating mutations in the leucine rich repeat kinase 2 (LRRK2) that cause and/or increase the risk for PD has led to the development of LRRK2 kinase inhibitors1,2,3. These have now entered clinical trials4. The exact function of LRRK2 is unclear, but a major advancement has been the identification of a subset of Rab GTPase proteins, including Rab10, as the first bona fide physiological substrates of the LRRK2 kinase5,6,7. Key challenges in the era of disease-modifying therapeutics are biochemical markers of LRRK2 kinase activation status and target engagement of LRRK2 kinase inhibitors.
So far, the principal pharmacokinetic marker for LRRK2 inhibitors in vivo has been a cluster of constitutively phosphorylated serine residues of LRRK2, in particular serine 935, that become dephosphorylated in response to diverse LRRK2 inhibitors8,9. However, serine 935 phosphorylation does not correlate with intrinsic cellular LRRK2 kinase activity because it is not directly phosphorylated by LRRK2 and is still phosphorylated in kinase-inactive LRRK210. LRRK2 kinase activity correlates well with autophosphorylation of serine 1292, but it is in practical terms not a suitable readout for endogenous LRRK2 kinase activity by immunoblot analysis of whole cell extracts due to the current lack of reliable and phosphospecific antibodies for this site10,11.
We have developed a robust and easy assay to quantify LRRK2 kinase pathway activity in human peripheral blood cells that measures LRRK2-controlled phosphorylation of its physiological target protein Rab10 at threonine 7311. Peripheral blood is easily accessible by venesection, which is a low risk and quick procedure that causes minimal discomfort. We focus on human peripheral blood neutrophils because they constitute an abundant (37&#8211;80% of all white blood cells) and homogeneous cell population that expresses relatively high levels of both LRRK2 and Rab1011. Furthermore, peripheral blood neutrophils can be isolated quickly and efficiently by employing an immunomagnetic negative approach. To ensure that the subsequent observed Rab10 phosphorylation is mediated by LRRK2, each batch of neutrophils is incubated with or without a potent and selective LRRK2 kinase inhibitor (we use and recommend MLi-2)2,12. This is then followed by cell lysis in a buffer containing the protease inhibitor diisopropyl fluorophosphate (DIFP), which is necessary for suppressing the intrinsic serine protease activity that is known to be high in neutrophils13. For the final analysis by quantitative immunoblotting, we recommend using the MJFF-pRab10 rabbit monoclonal antibody that specifically detects the Rab10 Thr73-phosphoepitope and does not cross-react with other phosphorylated Rab proteins14. Selectivity and specificity of this antibody has been validated in overexpression models of different Rab proteins and a A549 Rab10 knock-out cell line14. Thus, we measure the difference in Rab10 phosphorylation in neutrophil lysates that have been treated with and without a potent and selective LRRK2 kinase inhibitor2. Alternatively, samples could also be analyzed by other methods, such as quantitative mass spectrometry.
In conclusion, LRRK2-controlled Rab10 phosphorylation is a superior marker of LRRK2 kinase activity to LRRK2 phosphorylation at serine 935 and human peripheral blood neutrophils are a valuable resource for PD research into LRRK2. Our protocol provides a robust and easy assay to interrogate LRRK2 pathway activity in peripheral blood neutrophils and allows biochemical stratification of individuals with increased LRRK2 kinase activity15. Importantly, such individuals may benefit from future LRRK2 kinase inhibitor treatment.

<table border="0" cellpadding="0" cellspacing="0" style="width:979px;" width="978">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">1 mL Pipette tips</td>
			<td style="width:132px;">Sarstedt</td>
			<td style="width:95px;">70.762</td>
			<td style="width:432px;">or equivalent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">1.5 mL Micro tubes</td>
			<td style="width:132px;">Sarstedt</td>
			<td style="width:95px;">72.690.001</td>
			<td style="width:432px;">or equivalent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">10 mL Pipette tips&#160;</td>
			<td style="width:132px;">Sarstedt</td>
			<td style="width:95px;">86.1254.025&#160;</td>
			<td style="width:432px;">or equivalent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">10 &#956;L Pipette tips</td>
			<td style="width:132px;">Sarstedt</td>
			<td style="width:95px;">70.113</td>
			<td style="width:432px;">or equivalent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">15 mL falcon tube&#160;</td>
			<td style="width:132px;">Cellstar</td>
			<td style="width:95px;">188 271</td>
			<td style="width:432px;">or equivalent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">200 &#956;L Pipette tips</td>
			<td style="width:132px;">Sarstedt</td>
			<td style="width:95px;">70.760.002</td>
			<td style="width:432px;">or equivalent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">25 mL Pipette tips&#160;</td>
			<td style="width:132px;">Sarstedt</td>
			<td style="width:95px;">86.1685.001</td>
			<td style="width:432px;">or equivalent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">50 mL falcon tube&#160;</td>
			<td style="width:132px;">Cellstar</td>
			<td style="width:95px;">227 261</td>
			<td style="width:432px;">or equivalent</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:320px;">BD Vacutainer Hemogard Closure Plastic K2-EDTA Tube</td>
			<td style="width:132px;">BD&#160;</td>
			<td style="width:95px;">BD 367525</td>
			<td style="width:432px;">or equivalent</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:320px;">Beckman Coulter Allegra X-15R centrifuge</td>
			<td style="width:132px;">Beckman</td>
			<td style="width:95px;"></td>
			<td style="width:432px;">or equivalent centrifuge with swimging bucket rotator for 15 mL and 50 mL falcon tubes at speed 1000-1200 x g</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Category 2 biological safety cabinet.</td>
			<td style="width:132px;"></td>
			<td style="width:95px;"></td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:320px;">cOmplete(EDTA-free) protease inhibitor cocktail</td>
			<td style="width:132px;">Roche</td>
			<td style="width:95px;">11836170001</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:320px;">DIFP (Diisopropylfluorophosphate)&#160;</td>
			<td style="width:132px;">Sigma</td>
			<td style="width:95px;">D0879</td>
			<td style="width:432px;">Prepare 0.5M stock solution in isopropanol using special precautions&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Dimethyl sulfoxide&#160;</td>
			<td style="width:132px;">Sigma</td>
			<td style="width:95px;">6250</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Dry ice or liquid nitrogene</td>
			<td style="width:132px;"></td>
			<td style="width:95px;"></td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Dulbecco&#39;s phosphate-buffered saline&#160;</td>
			<td style="width:132px;">ThermoFisher</td>
			<td style="width:95px;">14190094</td>
			<td style="width:432px;">or equivalent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Easy 50 EasySep Magnet&#160;</td>
			<td style="width:132px;">Stemcell</td>
			<td style="width:95px;">18002</td>
			<td style="width:432px;">for holding 1 x 50ml conical tube</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:320px;">EasySep Direct Human Neutrophil Isolation Kit&#160;</td>
			<td style="width:132px;">Stemcell</td>
			<td style="width:95px;">19666</td>
			<td style="width:432px;">This contains Solutions called &#8220;Isolation Cocktail&#8221; and &#8220;RapidSpheres magnetic beads</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">EGTA</td>
			<td style="width:132px;">Sigma</td>
			<td style="width:95px;">E3889</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Eppendorf centrifuge 5417R centrifuge</td>
			<td style="width:132px;">Eppendorf</td>
			<td style="width:95px;"></td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Ethanol, in spray bottle</td>
			<td style="width:132px;"></td>
			<td style="width:95px;"></td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ethylenediaminetetraacetic acid&#160;</td>
			<td style="width:132px;">Sigma</td>
			<td style="width:95px;">E6758</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Ice</td>
			<td style="width:132px;"></td>
			<td style="width:95px;"></td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Isopropanol (anhydrous grade)&#160;</td>
			<td style="width:132px;">Sigma</td>
			<td style="width:95px;">278475</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="168">
			<td height="168" style="height:168px;width:320px;">Lysis buffer (50 mM Tris-HCl pH 7.5, 1%(v/v) Triton X-100, 1 mM EGTA, 1 mM Na3VO4, 50 mM NaF, 10 mM &#946;-glycerophosphate, 5 mM sodium pyrophosphate, 0.27 M sucrose, 0.1% (v/v) &#946;-mercaptoethanol, 1x cOmplete(EDTA-free) protease inhibitor cocktail (Roche), 1 &#956;g/ml Microcystin-LR, 0.5 mM diisopropylfluorophosphate (DIFP).&#160;</td>
			<td style="width:132px;"></td>
			<td style="width:95px;"></td>
			<td style="width:432px;">alternatively frozen lysis buffer in aliquots without Microcystin-LR, DIFP available from MRC-PPU Reagents (http://mrcppureagents.dundee.ac.uk/)</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:320px;">Merck LRRK2 inhibitor II (MLi-2)</td>
			<td style="width:132px;">Merck</td>
			<td style="width:95px;">438194-10MG</td>
			<td style="width:432px;">or equivalent (potent and selective LRRK2 inhinitor)</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:320px;">Microcystin-LR</td>
			<td style="width:132px;">Enzo Life Sciences</td>
			<td style="width:95px;">ALX-350-012-M001</td>
			<td style="width:432px;">1 mg/ml stock in DMSO and store at -80 oC.&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Na3VO4</td>
			<td style="width:132px;">Aldrich</td>
			<td style="width:95px;">450243</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">NaF</td>
			<td style="width:132px;">Sigma</td>
			<td style="width:95px;">S7920</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Odyssey CLx scan Western Blot imaging system</td>
			<td style="width:132px;">Odyssey</td>
			<td style="width:95px;"></td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Permanent marker pen</td>
			<td style="width:132px;"></td>
			<td style="width:95px;"></td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Personal protection equipment</td>
			<td style="width:132px;"></td>
			<td style="width:95px;"></td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">RPMI 1640 Medium&#160;</td>
			<td style="width:132px;">ThermoFisher</td>
			<td style="width:95px;">21875034</td>
			<td style="width:432px;">or equivalent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">sodium pyrophosphate</td>
			<td style="width:132px;">Sigma</td>
			<td style="width:95px;">S22</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">sucrose</td>
			<td style="width:132px;">Sigma</td>
			<td style="width:95px;">S0389</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">&#946;-glycerophosphate</td>
			<td style="width:132px;">Sigma</td>
			<td style="width:95px;">50020</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">&#946;-mercaptoethanol</td>
			<td style="width:132px;">Sigma</td>
			<td style="width:95px;">M3148</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Suggested antibodies for Western blotting</td>
			<td style="width:132px;"></td>
			<td style="width:95px;"></td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Anti-RAB10 (phospho T73) antibody [MJF-R21]</td>
			<td style="width:132px;">abcam</td>
			<td style="width:95px;">ab230261</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:320px;">Anti-&#945;-tubulin</td>
			<td style="width:132px;">Cell Signaling Technologies</td>
			<td style="width:95px;">5174</td>
			<td style="width:432px;">used at 1:2000 dilution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Goat anti-mouse IRDye 680LT</td>
			<td style="width:132px;">LI-COR</td>
			<td style="width:95px;">926-68020</td>
			<td style="width:432px;">used at 1:10,000 dilution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Goat anti-mouse IRDye 800CW</td>
			<td style="width:132px;">LI-COR</td>
			<td style="width:95px;">926-32210</td>
			<td style="width:432px;">used at 1:10,000 dilution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Goat anti-rabbit IRDye 800CW</td>
			<td style="width:132px;">LI-COR</td>
			<td style="width:95px;">926-32211</td>
			<td style="width:432px;">used at 1:10,000 dilution</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:320px;">MJFF-total Rab10 mouse antibody</td>
			<td style="width:132px;">generated by nanoTools (nanotools.de)</td>
			<td style="width:95px;">not applicable*</td>
			<td style="width:432px;">used at 2 &#956;g/ml final concentration; * The MJFF-total Rab10 antibody generated by nanoTools (www.nanotools.de) [11] will be commercialised by the Michael J Fox Foundation in 2018</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:320px;">Mouse anti-LRRK2 C-terminus antibody</td>
			<td style="width:132px;">Antibodies Incorporated</td>
			<td style="width:95px;">&#160;75-253</td>
			<td style="width:432px;">used at 1 &#956;g/ml final concentration</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:320px;">pS935-LRRK2</td>
			<td style="width:132px;">MRC PPU Reagents and Services</td>
			<td style="width:95px;">UDD2</td>
			<td style="width:432px;">MJFF-total Rab10 mouse antibody</td>
		</tr>
	</tbody>
</table>

human peripheral blood neutrophil isolation for interrogating the parkinson's associated lrrk2 kinase pathway by assessing rab10 phosphorylation

The leucine rich repeat kinase 2 (LRRK2) is the most frequently mutated gene in hereditary Parkinson&#8217; disease (PD) and all pathogenic LRRK2 mutations result in hyperactivation of its kinase function. Here, we describe an easy and robust assay to quantify LRRK2 kinase pathway activity in human peripheral blood neutrophils by measuring LRRK2-controlled phosphorylation of one of its physiological substrates, Rab10 at threonine 73. The immunoblotting analysis described requires a fully selective and phosphospecific antibody that recognizes the Rab10 Thr73 epitope phosphorylated by LRRK2, such as the MJFF-pRab10 rabbit monoclonal antibody. It uses human peripheral blood neutrophils, because peripheral blood is easily accessible and neutrophils are an abundant and homogenous constituent. Importantly, neutrophils express relatively high levels of both LRRK2 and Rab10. A potential drawback of neutrophils is their high intrinsic serine protease activity, which necessitates the use of very potent protease inhibitors such as the organophosphorus neurotoxin diisopropylfluorophosphate (DIFP) as part of the lysis buffer. Nevertheless, neutrophils are a valuable resource for research into LRRK2 kinase pathway activity in vivo and should be considered for inclusion into PD biorepository collections.

Our assay allows interrogating the activation of the PD-associated LRRK2 kinase in human peripheral blood neutrophils with LRRK2-dependent Rab10 phosphorylation as a readout. Neutrophils are a homogenous and abundant peripheral white blood cell population that expresses high levels of both the LRRK2 and Rab10 proteins (Figure 1). The only other cell population among the remaining peripheral blood mononuclear cells (PBMCs) with high copy numbers of both proteins are monocytes, but these make ...

Watch this Scientific Journal Video about Human Peripheral Blood Neutrophil Isolation for Interrogating the Parkinson's Associated LRRK2 Kinase Pathway by Assessing Rab10 Phosphorylation at JoVE.com

Human Peripheral Blood Neutrophil Isolation for Interrogating the Parkinson's Associated LRRK2 Kinase Pathway by Assessing Rab10 Phosphorylation

Mutations in the leucine rich repeat kinase 2 gene (LRRK2) cause hereditary Parkinson&#8217;s disease. We have developed an easy and robust method for assessing LRRK2-controlled phosphorylation of Rab10 in human peripheral blood neutrophils. This may help identify individuals with increased LRRK2 kinase pathway activity.

The leucine rich repeat kinase 2 (LRRK2) is the most frequently mutated gene in hereditary Parkinson&#8217; disease (PD) and all pathogenic LRRK2 ...

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Biochemistry

7.3K Views.  University of Dundee. Mutations in the leucine rich repeat kinase 2 gene (LRRK2) cause hereditary Parkinson’s disease. We have developed an easy and robust method for assessing LRRK2-controlled phosphorylation of Rab10 in human peripheral blood neutrophils. This may help identify individuals with increased LRRK2 kinase pathway activity.

Video: Human Peripheral Blood Neutrophil Isolation for Interrogating the Parkinson's Associated LRRK2 Kinase Pathway by Assessing Rab10 Phosphorylation

Assaying Protein Kinase Activity with Radiolabeled ATP

Protein kinases are able to govern large-scale cellular changes in response to complex arrays of stimuli, and much effort has been directed at uncovering allosteric details of their regulation. Kinases comprise signaling networks whose defects are often hallmarks of multiple forms of cancer and related diseases, making an assay platform amenable to manipulation of upstream regulatory factors and validation of reaction requirements critical in the search for improved therapeutics. Here, we describe a basic kinase assay that can be easily adapted to suit specific experimental questions including but not limited to testing the effects of biochemical and pharmacological agents, genetic manipulations such as mutation and deletion, as well as cell culture conditions and treatments to probe cell signaling mechanisms. This assay utilizes radiolabeled [&#947;-32P] ATP, which allows for quantitative comparisons and clear visualization of results, and can be modified for use with immunoprecipitated or recombinant kinase, specific or typified substrates, all over a wide range of reaction conditions.

Protein kinases are highly evolved signaling enzymes and scaffolds that are critical for inter- and intracellular signal transduction. We present a protocol for measuring kinase activity through the use of radiolabeled adenosine triphosphate ([&#947;-32P] ATP), a reliable method to aid in elucidation of cellular signaling regulation.

Protein kinases are able to govern large-scale cellular changes in response to complex arrays of stimuli, and much effort has been directed at uncovering ...

Oligopeptide Competition Assay for Phosphorylation Site Determination

Protein phosphorylation at specific sites determines its conformation and interaction with other molecules. Thus, protein phosphorylation affects biological functions and characteristics of the cell. Currently, the most common method for discovering phosphorylation sites is by liquid chromatography/mass spectrometry (LC/MS) analysis, a rapid and sensitive method. However, relatively labile phosphate moieties are often released from phosphopeptides during the fragmentation step, which often yields false-negative signals. In such cases, a traditional in vitro kinase assay using site-directed mutants would be more accurate, but this method is laborious and time-consuming. Therefore, an alternative method using peptide competition may be advantageous. The consensus recognition motif of 5&#39; adenosine monophosphate-activated protein kinase (AMPK) has been established1 and was validated using a positional scanning peptide library assay2. Thus, AMPK phosphorylation sites for a novel substrate could be predicted and confirmed by the peptide competition assays. In this report, we describe the detailed steps and procedures for the in vitro oligopeptide-competing kinase assay by illustrating AMPK-mediated nuclear factor erythroid 2-related factor 2 (Nrf2) phosphorylation. To authenticate the phosphorylation site, we carried out a sequential in vitro kinase assay using a site-specific mutant. Overall, the peptide competition assay provides a method to screen multiple potential phosphorylation sites and to identify sites for validation by the phosphorylation site mutants.

Peptide competition assays are widely used in a variety of molecular and immunological experiments. This paper describes a detailed method for an in vitro oligopeptide-competing kinase assay and the associated validation procedures, which may be useful to find specific phosphorylation sites.

Protein phosphorylation at specific sites determines its conformation and interaction with other molecules. Thus, protein phosphorylation affects ...

Rab10 Phosphorylation Detection by LRRK2 Activity Using SDS-PAGE with a Phosphate-binding Tag

Mutations in leucine-rich repeat kinase 2 (LRRK2) have been shown to be linked with familial Parkinson&#39;s disease (FPD). Since abnormal activation of the kinase activity of LRRK2 has been implicated in the pathogenesis of PD, it is essential to establish a method to evaluate the physiological levels of the kinase activity of LRRK2. Recent studies revealed that LRRK2 phosphorylates members of the Rab GTPase family, including Rab10, under physiological conditions. Although the phosphorylation of endogenous Rab10 by LRRK2 in cultured cells could be detected by mass spectrometry, it has been difficult to detect it by immunoblotting due to the poor sensitivity of currently available phosphorylation-specific antibodies for Rab10. Here, we describe a simple method of detecting the endogenous levels of Rab10 phosphorylation by LRRK2 based on immunoblotting utilizing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) combined with a phosphate-binding tag (P-tag), which is N-(5-(2-aminoethylcarbamoyl)pyridin-2-ylmetyl)-N,N&#39;,N&#39;-tris(pyridin-2-yl-methyl)-1,3-diaminopropan-2-ol. The present protocol not only provides an example of the methodology utilizing the P-tag but also enables the assessment of how mutations as well as inhibitor treatment/administration or any other factors alter the downstream signaling of LRRK2 in cells and tissues.

The present study describes a simple method of detecting endogenous levels of Rab10 phosphorylation by leucine-rich repeat kinase 2.

Mutations in leucine-rich repeat kinase 2 (LRRK2) have been shown to be linked with familial Parkinson&#39;s disease (FPD). Since abnormal activation of ...

Protein Digestion, Ultrafiltration, and Size Exclusion Chromatography to Optimize the Isolation of Exosomes from Human Blood Plasma and Serum

Exosomes, a type of nanovesicle released from all cell types, can be isolated from any bodily fluid. The contents of exosomes, including proteins and RNAs, are unique to the cells from which they are derived and can be used as indicators of disease. Several common enrichment protocols, including ultracentrifugation, yield exosomes laden with soluble protein contaminants. Specifically, we have found that the most abundant proteins within blood often co-purify with exosomes and can confound downstream proteomic studies, thwarting the identification of low abundance biomarker candidates. Of additional concern is irreproducibility of exosome protein quantification due to inconsistent representation of non-exosomal protein levels. The protocol detailed here was developed to remove non-exosomal proteins that co-purify along with exosomes, adding rigor to the exosome purification process. Five methods were compared using paired blood plasma and serum from five donors. Analysis using nanoparticle tracking analysis and micro bicinchoninic acid protein assay revealed that a combined protocol utilizing ultrafiltration and size exclusion chromatography yielded the optimal vesicle enrichment and soluble protein removal. Western blotting was used to verify that the expected abundant blood proteins, including albumin and apolipoproteins, were depleted.

Here, we present a protocol to purify exosomes from both plasma and serum with reduced co-purification of non-exosomal blood proteins. The optimized protocol includes ultrafiltration, protease treatment, and size exclusion chromatography. Enhanced purification of exosomes benefits downstream analyses, including more accurate quantification of vesicles and proteomic characterization.

Exosomes, a type of nanovesicle released from all cell types, can be isolated from any bodily fluid. The contents of exosomes, including proteins and ...

Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay

Cyclin-dependent kinase 1 (Cdk1) is a master controller for the cell cycle in all eukaryotes and phosphorylates an estimated 8 - 13% of the proteome; however, the number of identified targets for Cdk1, particularly in human cells is still low. The identification of Cdk1-specific phosphorylation sites is important, as they provide mechanistic insights into how Cdk1 controls the cell cycle. Cell cycle regulation is critical for faithful chromosome segregation, and defects in this complicated process lead to chromosomal aberrations and cancer.
Here, we describe an in vitro kinase assay that is used to identify Cdk1-specific phosphorylation sites. In this assay, a purified protein is phosphorylated in vitro by commercially available human Cdk1/cyclin B. Successful phosphorylation is confirmed by SDS-PAGE, and phosphorylation sites are subsequently identified by mass spectrometry. We also describe purification protocols that yield highly pure and homogeneous protein preparations suitable for the kinase assay, and a binding assay for the functional verification of the identified phosphorylation sites, which probes the interaction between a classical nuclear localization signal (cNLS) and its nuclear transport receptor karyopherin &#945;. To aid with experimental design, we review approaches for the prediction of Cdk1-specific phosphorylation sites from protein sequences. Together these protocols present a very powerful approach that yields Cdk1-specific phosphorylation sites and enables mechanistic studies into how Cdk1 controls the cell cycle. Since this method relies on purified proteins, it can be applied to any model organism and yields reliable results, especially when combined with cell functional studies.

Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay

Cyclin-dependent kinase 1 (Cdk1) is activated in the G2 phase of the cell cycle and regulates many cellular pathways. Here, we present a protocol for an in vitro kinase assay with Cdk1, which allows the identification of Cdk1-specific phosphorylation sites for establishing cellular targets of this important kinase.

Cyclin-dependent kinase 1 (Cdk1) is a master controller for the cell cycle in all eukaryotes and phosphorylates an estimated 8 - 13% of the proteome; ...

Studying RNA Interactors of Protein Kinase RNA-Activated during the Mammalian Cell Cycle

Protein kinase RNA-activated (PKR) is a member of the innate immune response proteins and recognizes the double-stranded secondary structure of viral RNAs. When bound to viral double-stranded RNAs (dsRNAs), PKR undergoes dimerization and subsequent autophosphorylation. Phosphorylated PKR (pPKR) becomes active and induces phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2&#945;) to suppress global translation. Increasing evidence suggests that PKR can be activated under physiological conditions such as during the cell cycle or under various stress conditions without infection. However, our understanding of the RNA activators of PKR is limited due to the lack of a standardized experimental method to capture and analyze PKR-interacting dsRNAs. Here, we present an experimental protocol to specifically enrich and analyze PKR bound RNAs during the cell cycle using HeLa cells. We utilize the efficient crosslinking activity of formaldehyde to fix PKR-RNA complexes and isolate them via immunoprecipitation. PKR co-immunoprecipitated RNAs can then be further processed to generate a high-throughput sequencing library. One major class of PKR-interacting cellular dsRNAs is mitochondrial RNAs (mtRNAs), which can exist as intermolecular dsRNAs through complementary interaction between the heavy-strand and the light-strand RNAs. To study the strandedness of these duplex mtRNAs, we also present a protocol for strand-specific qRT-PCR. Our protocol is optimized for the analysis of PKR-bound RNAs, but it can be easily modified to study cellular dsRNAs or RNA-interactors of other dsRNA binding proteins.

We present experimental approaches for studying RNA-interactors of double-stranded RNA binding protein kinase RNA-activated (PKR) during the mammalian cell cycle using HeLa cells. This method utilizes formaldehyde to crosslink RNA-PKR complexes and immunoprecipitation to enrich PKR-bound RNAs. These RNAs can be further analyzed through high-throughput sequencing or qRT-PCR.

Protein kinase RNA-activated (PKR) is a member of the innate immune response proteins and recognizes the double-stranded secondary structure of viral ...

Enhancing the Engraftment of Human Induced Pluripotent Stem Cell-derived Cardiomyocytes via a Transient Inhibition of Rho Kinase Activity

A crucial factor in improving cellular therapy effectiveness for myocardial regeneration is to safely and efficiently increase the cell engraftment rate. Y-27632 is a highly potent inhibitor of Rho-associated, coiled-coil-containing protein kinase (RhoA/ROCK) and is used to prevent dissociation-induced cell apoptosis (anoikis). We demonstrate that Y-27632 pretreatment for human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs+RI) prior to implantation results in a cell engraftment rate improvement in a mouse model of acute myocardial infarction (MI). Here, we describe a complete procedure of hiPSC-CMs differentiation, purification, and cell pretreatment with Y-27632, as well as the resulting cell contraction, calcium transient measurements, and transplantation into mouse MI models. The proposed method provides a simple, safe, effective, and low-cost method which significantly increases the cell engraftment rate. This method cannot only be used in conjunction with other methods to further enhance the cell transplantation efficiency but also provides a favorable basis for the study of the mechanisms of other cardiac diseases.

In this protocol, we demonstrate and elaborate on how to use human induced pluripotent stem cells for cardiomyocyte differentiation and purification, and further, on how to improve its transplantation efficiency with Rho-associated protein kinase inhibitor pretreatment in a mouse myocardial infarction model.

A crucial factor in improving cellular therapy effectiveness for myocardial regeneration is to safely and efficiently increase the cell engraftment rate. ...

Translating Ribosome Affinity Purification (TRAP) for RNA Isolation from Endothelial Cells In Vivo

Many studies have been limited to using in vitro cellular assays and whole tissues or isolating of specific cell types from animals for in vitro analysis of transcriptome and gene expression by qPCR and RNA sequencing. Comprehensive transcriptome and gene expression analysis of specific cell types in complex tissues and organs will be critical to understand cellular and molecular mechanisms by which genes are regulated and their association with tissue homeostasis and organ functions. In this article, we demonstrate the methodology for isolation of ribosome-bound RNA directly in vivo in the vascular endothelia of animal lungs as an example. The specific materials and procedures for tissue processing and RNA purification will be described, including the assessment of RNA quality and yield as well as real time qPCR for arteriogenic gene assays. This approach, known as translating ribosome affinity purification (TRAP) technique, can be utilized for characterization of gene expression and transcriptome analysis of certain cell types directly in vivo in any specific type in complex tissues.

Translating Ribosome Affinity Purification TRAP for RNA Isolation from Endothelial Cells In Vivo

We present an approach to purify ribosome-bound mRNA from vascular endothelial cells (ECs) directly in mouse brain, lung and heart tissues via EC-specific genetic tag of enhanced green fluorescence protein (EGFP)in ribosomes in combination with RNA purification.

Many studies have been limited to using in vitro cellular assays and whole tissues or isolating of specific cell types from animals for in vitro analysis ...

Kinase Inhibitor Screening In Self-assembled Human Protein Microarrays

The screening of kinase inhibitors is crucial for better understanding properties of a drug and for the identification of potentially new targets with clinical implications. Several methodologies have been reported to accomplish such screening. However, each has its own limitations (e.g., the screening of only ATP analogues, restriction to using purified kinase domains, significant costs associated with testing more than a few kinases at a time, and lack of flexibility in screening protein kinases with novel mutations). Here, a new protocol that overcomes some of these limitations and can be used for the unbiased screening of kinase inhibitors is presented. A strength of this method is its ability to compare the activity of kinase inhibitors across multiple proteins, either between different kinases or different variants of the same kinase. Self-assembled protein microarrays generated through the expression of protein kinases by a human-based in vitro transcription and translation system (IVTT) are employed. The proteins displayed on the microarray are active, allowing for measurement of the effects of kinase inhibitors. The following procedure describes the protocol steps in detail, from the microarray generation and screening to the data analysis.

A detailed protocol for the generation of self-assembled human protein microarrays for the screening of kinase inhibitors is presented.

The screening of kinase inhibitors is crucial for better understanding properties of a drug and for the identification of potentially new targets with ...

Nonradioactive Assay to Measure Polynucleotide Phosphorylation of Small Nucleotide Substrates

Polynucleotide kinases (PNKs) are enzymes that catalyze the phosphorylation of the 5&#39; hydroxyl end of DNA and RNA oligonucleotides. The activity of PNKs can be quantified using direct or indirect approaches. Presented here is a direct, in vitro approach to measure PNK activity that relies on a fluorescently-labeled oligonucleotide substrate and polyacrylamide gel electrophoresis. This approach provides resolution of the phosphorylated products while avoiding the use of radiolabeled substrates. The protocol details how to set up the phosphorylation reaction, prepare and run large polyacrylamide gels, and quantify the reaction products. The most technically challenging part of this assay is pouring and running the large polyacrylamide gels; thus, important details to overcome common difficulties are provided. This protocol was optimized for Grc3, a PNK that assembles into an obligate pre-ribosomal RNA processing complex with its binding partner, the Las1 nuclease. However, this protocol can be adapted to measure the activity of other PNK enzymes. Moreover, this assay can also be modified to determine the effects of different components of the reaction, such as the nucleoside triphosphate, metal ions, and oligonucleotides.

This protocol describes a nonradioactive assay to measure kinase activity of polynucleotide kinases (PNKs) on small DNA and RNA substrates.

Polynucleotide kinases (PNKs) are enzymes that catalyze the phosphorylation of the 5&#39; hydroxyl end of DNA and RNA oligonucleotides. The activity of ...