The authors are thankful to Dr. Jeffrey Golden (Cedars-Sinai Medical Center) for the critical review of the manuscript. This work was funded in part by the National Institute of Neurological Disease and Stroke (NINDS, R01NS113516).

1. Cell maintenance and seeding (Day 1)
<ol>
	<li>Maintain HEK293T cells in cell culture media containing Dulbecco&#39;s Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS) (in 100 mm culture dishes) in a humidified incubator at 37 &#176;C with 5% CO2.</li>
	<li>Before starting, check the confluency of the plate by viewing under the microscope. When the cells reach approximately 80-90% confluency, prepare to seed the cells in a 6-well culture plate by removing the media and washing with 10 mL of Dulbecco&#39;s phosphate-buffered saline (DPBS).</li>
	<li>Remove the DPBS from the culture dish and treat the cells with 1 mL of 0.05% Trypsin-EDTA phenol red. Incubate for 3 min, then take out the plate from the incubator and add 9 mL of culture media (DMEM with 10% FBS) to stop the trypsin reaction. Slowly pipette up and down to ensure any cells still stuck to the plate are dislodged. Transfer the cell suspension to a 50 mL tube.</li>
	<li>Centrifuge at 300 &#215; g for 5 min at room temperature. Remove the media and resuspend the cell pellets with 1 mL of fresh media (DMEM + 10% FBS).</li>
	<li>Count the number of cells using a hemocytometer.
	<ol>
		<li>Ensure even distribution of cells by gently swirling the tube. Immediately take out 10 &#181;L of the cell suspension and place into a 1.7 mL microcentrifuge tube. Add 90 &#181;L of media to the same tube.</li>
		<li>After mixing the cells and media gently, take the cell suspension and apply 10 &#181;L to each of the chambers of the hemocytometer by gently pipetting underneath the coverslip.</li>
		<li>Using a 10x objective, focus the grid lines of the hemocytometer under a microscope. Once focused, count the number of cells in one set of 16 squares (4 x 4 squares) using a hand tally counter. Repeat until all four sets of 16 squares are counted.</li>
		<li>Calculate the total number of cells/mL by taking the average cell count (from each of 16 corner squares) and multiplying that by 105. 
		NOTE: Instead of using a hemocytometer to count cells, an automated cell counter can be used according to the manufacturer&#39;s instructions.</li>
	</ol>
	</li>
	<li>Once cell counting is completed, prepare to plate cells in a 6-well plate at 7.5 &#215; 105 cells/well density with 2 mL of media/well. In a 50 mL tube, add the necessary volume of cells along with 13 mL of media. Dispense 2 mL of the diluted cell suspension into each of the 6 wells.
	<ol>
		<li>Before plating, calculate the number of cells necessary for 7.5 &#215; 105 cells/well using C1V1 = C2V2 where C1 is the initial cell count (cell number/mL), V1 is the volume needed from the initial cell suspension, C2 is the desired target cell density (cell number/mL), and V2 is the final volume needed for cell seeding.</li>
	</ol>
	</li>
	<li>After dispensing, tap the plate gently on all sides to spread the cells and then place it in a humidified incubator at 37 &#176;C with 5% CO2 overnight.</li>
</ol>
2. Polyethyleneimine (PEI)-mediated cell transfection and post transfection cell seeding (Day 2)
<ol>
	<li>Remove the 6-well plate from the incubator and aspirate out the existing culture media from each well. Add 2 mL of fresh media per well.</li>
	<li>Transfect the cells with split-Rluc plasmid DNA (pCAG-MitoRlucN-T2A-RlucCER-IRES-mCherry) dissolved in TE buffer (pH 8.0).
	<ol>
		<li>For each well, mix the DNA (750 ng) and PEI (ratio of DNA/PEI = 1:3) in 200 &#181;L of DMEM in a 1.7 mL microcentrifuge tube. Quickly vortex the DNA/PEI at level 8 for approximately 2 s to ensure they mix well together to form complex. After that, spin it down in a mini centrifuge briefly (&#60;3 s).</li>
		<li>Let the mixture of DNA/PEI incubate at room temperature for 15 min and then add the mixture (by dropping it) to the surface of the culture media in the 6-well plate containing cells. Tap the plate gently (to evenly distribute the mixture) and incubate it in a humidified incubator at 37 &#176;C with 5% CO2 for 6 h.</li>
	</ol>
	</li>
	<li>While incubating, prepare a Poly-D-Lysine (PDL)-coated 96-well plate by first adding 70 &#181;L of PDL (50 &#181;g/mL in DPBS) to each well and incubating in a humidified incubator at 37 &#176;C with 5% CO2 for at least 1 h. Remove the PDL solution and then wash each well 2x with 100 &#181;L of DPBS. At the end of the second wash, ensure that all the remaining DPBS is removed.</li>
	<li>At 6 h post transfection, prepare to seed the transfected cells in a PDL-coated 96-well plate.
	<ol>
		<li>Take out the 6-well plate containing transfected cells from the incubator, aspirate out the media, and wash each well with 2 mL of DPBS. After removing the DPBS, add 350 &#181;L of 0.05% Trypsin-EDTA phenol red and incubate for 1-2 min. To stop the trypsin reaction, add 1.7 mL of media to each well.</li>
		<li>After transferring the cells along with media to a 50 mL tube, spin the tube at 300 &#215; g for 5 min in a tabletop centrifuge. Aspirate the media and resuspend the cell pellet with 1 mL of fresh media. Count the number of cells using a hemocytometer (as described in step 1.5).</li>
	</ol>
	</li>
	<li>Seed the cells in a PDL-coated 96-well plate at a density of 4 &#215; 104 cells/well in 100 &#181;L of culture media. For this, in a 50 mL tube, add the necessary volume of cells (see below for calculation) along with appropriate volume of media (12 mL total volume). Using a multichannel pipette, dispense 100 &#181;L of the diluted cell suspension into each of the 96 wells. Incubate the cells for 18 h in a humidified incubator at 37 &#176;C with 5% CO2.
	<ol>
		<li>Calculate the number of cells necessary for 4 &#215; 104 cells/well using C1V1 = C2V2 where C1 is the initial cell count (cell number/mL), V1 is the volume needed from the initial cell suspension, C2 is the desired target cell density (cell number/mL), and V2 is the final volume needed for cell seeding.</li>
	</ol>
	</li>
</ol>
3. Chemical treatment and luciferase assay in live cells (Day 3)
<ol>
	<li>In a 1.7 mL microfuge tube, prepare the three fresh solutions of 50 &#181;M Rhosin (50 mM stock in DMSO), 25 &#181;M Ehop-016 (25 mM stock in DMSO), and 50 &#181;M ZCL278 (50 mM stock in DMSO) by diluting each stock solution (50 mM Rhosin, 25 mM Ehop-016, and 50 mL ZCL278; all in DMSO) 1:1,000 in the required amount (50 &#181;L/well &#215; number of wells) of culture media. To each solution, add live cell substrate (50 mM stock in DMSO) for Renilla luciferase diluted 1:2,000 to a final concentration of 25&#160;&#181;M. To make 0.5, 5, and 50 &#181;M ZCL278 solutions, perform serial dilutions using the initial 50 &#181;M ZCL278 in culture media. 
	NOTE: If the chemical incubation time is desired for less than 1-1.5 h, the cells can be preincubated with live cell substrate (for Renilla luciferase) for 1-1.5 h before they are treated with each chemical. We add chemicals and live cell substrate simultaneously to optimize the protocol for high-throughput drug screening.</li>
	<li>Remove the media from each well of the 96-well plate containing transfected cells and add 50 &#181;L of chemical and substrate media mixture to each well.</li>
	<li>After incubating the cells for 1 h, 2 h, or 5 h, take out the culture plate from the incubator, load it onto the luminescence plate reader, and measure luminescence.
	<ol>
		<li>Before starting, ensure that the plate reader is turned on. Access the microplate reader software and create a new file by clicking New Session. Set the temperature of the plate reader to 37 &#176;C by clicking Incubator, checking the temperature option, and typing in 37 &#176;C. Under Plate Layout, choose the option Unknown and specify the wells to measure by clicking and dragging.</li>
		<li>Under Protocol, click Luminescence and keep to the default settings. Once finished with the setup, load the plate with the lid off into the plate reader and choose Run Plate In. Click Start and save file window will appear. Save the file to your desktop by renaming it and clicking Save. 
		NOTE: The luminescence will continue to be produced for &#62;24 h after the addition of the live cell substrate.</li>
	</ol>
	</li>
	<li>Once the reading is complete, remove&#160;the plate from the plate reader and then click Run Plate In to put the reader back in. Once completed, place the plate back in the humidified incubator (37 &#176;C, 5% CO2) until the next reading.</li>
	<li>When finished, transfer the luminescence data to a graphing program to plot relative luminescence unit (RLU) (y-axis) for each variable (e.g., chemicals or concentrations) (x-axis) and analyze the data.</li>
</ol>
4. Validation of split-Rluc assay with other methods.
<ol>
	<li>Perform other assays such as proximity ligation assay (PLA), transmission electron microscopy, and mitochondrial calcium uptake monitoring to validate the results obtained from split-Rluc assay as described previously24.</li>
</ol>

A Simple Assay to Measure ER-Mitochondria Contacts for High-Throughput Screens

<ol>
	<li>Aoyama-Ishiwatari, S., Hirabayashi, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Endoplasmic+reticulum-mitochondria+contact+sites-emerging+intracellular+signaling+hubs.">Endoplasmic reticulum-mitochondria contact sites-emerging intracellular signaling hubs.</a> Front Cell Dev Biol. 9, 653828 (2021).</li><li>Sassano, M. L., Felipe-Abrio, B., Agostinis, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ER-mitochondria+contact+sites;+a+multifaceted+factory+for+Ca2++signaling+and+lipid+transport.">ER-mitochondria contact sites; a multifaceted factory for Ca2+ signaling and lipid transport.</a> Front Cell Dev Biol. 10, 988014 (2022).</li><li>Scorrano, L., 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=Coming+together+to+define+membrane+contact+sites.">Coming together to define membrane contact sites.</a> Nat Commun. 10 (1), 1287 (2019).</li><li>Voeltz, G. K., Sawyer, E. M., Hajn&#243;czky, G., Prinz, W. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Making+the+connection:+How+membrane+contact+sites+have+changed+our+view+of+organelle+biology.">Making the connection: How membrane contact sites have changed our view of organelle biology.</a> Cell. 187 (2), 257-270 (2024).</li><li>Paillusson, S., 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=There's+something+wrong+with+my+MAM;+the+ER-mitochondria+axis+and+neurodegenerative+diseases.">There's something wrong with my MAM; the ER-mitochondria axis and neurodegenerative diseases.</a> Trends Neurosci. 39 (3), 146-157 (2016).</li><li>Sasi, U. S. S., Sindhu, G., Raj, P. S., Raghu, K. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondria+associated+membranes+(MAMs):+emerging+drug+targets+for+diabetes.">Mitochondria associated membranes (MAMs): emerging drug targets for diabetes.</a> Curr Med Chem. 27 (20), 3362-3385 (2019).</li><li>Joshi, A. U., Kornfeld, O. S., Mochly-Rosen, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+entangled+ER-mitochondrial+axis+as+a+potential+therapeutic+strategy+in+neurodegeneration:+A+tangled+duo+unchained.">The entangled ER-mitochondrial axis as a potential therapeutic strategy in neurodegeneration: A tangled duo unchained.</a> Cell Calcium. 60 (3), 218-234 (2016).</li><li>Moltedo, O., Remondelli, P., Amodio, 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+mitochondria-endoplasmic+reticulum+contacts+and+their+critical+role+in+aging+and+age-associated+diseases.">The mitochondria-endoplasmic reticulum contacts and their critical role in aging and age-associated diseases.</a> Front Cell Dev Biol. 7, 172 (2019).</li><li>Rieusset, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+endoplasmic+reticulum-mitochondria+contact+sites+in+the+control+of+glucose+homeostasis:+an+update.">The role of endoplasmic reticulum-mitochondria contact sites in the control of glucose homeostasis: an update.</a> Cell Death Dis. 9 (3), 388 (2018).</li><li>Bouguerra, M. D., Lalli, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ER-mitochondria+interactions:+Both+strength+and+weakness+within+cancer+cells.">ER-mitochondria interactions: Both strength and weakness within cancer cells.</a> Biochim Biophys Acta Mol Cell Res. 1866 (4), 650-662 (2019).</li><li>Tepikin, A. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+junctions+with+cellular+organelles:+Ca2++signalling+perspective.">Mitochondrial junctions with cellular organelles: Ca2+ signalling perspective.</a> Pfl&#252;gers Arch. 470 (8), 1181-1192 (2018).</li><li>Masson, G. L., Przedborski, S., Abbott, L. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+computational+model+of+motor+neuron+degeneration.">A computational model of motor neuron degeneration.</a> Neuron. 83 (4), 975-988 (2014).</li><li>Giamogante, F., Barazzuol, L., Brini, M., Cal&#236;, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ER-mitochondria+contact+sites+reporters:+strengths+and+weaknesses+of+the+available+approaches.">ER-mitochondria contact sites reporters: strengths and weaknesses of the available approaches.</a> Int J Mol Sci. 21 (21), 8157 (2020).</li><li>Rizzuto, 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=Close+contacts+with+the+endoplasmic+reticulum+as+determinants+of+mitochondrial+Ca2++responses.">Close contacts with the endoplasmic reticulum as determinants of mitochondrial Ca2+ responses.</a> Science. 280 (5370), 1763-1766 (1998).</li><li>Valm, A. 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=Applying+systems-level+spectral+imaging+and+analysis+to+reveal+the+organelle+interactome.">Applying systems-level spectral imaging and analysis to reveal the organelle interactome.</a> Nature. 546 (7656), 162-167 (2017).</li><li>Csord&#225;s, 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=Imaging+interorganelle+contacts+and+local+calcium+dynamics+at+the+ER-mitochondrial+interface.">Imaging interorganelle contacts and local calcium dynamics at the ER-mitochondrial interface.</a> Mol Cell. 39 (1), 121-132 (2010).</li><li>Cieri, 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=SPLICS:+a+split+green+fluorescent+protein-based+contact+site+sensor+for+narrow+and+wide+heterotypic+organelle+juxtaposition.">SPLICS: a split green fluorescent protein-based contact site sensor for narrow and wide heterotypic organelle juxtaposition.</a> Cell Death Differ. 25 (6), 1131-1145 (2018).</li><li>Kakimoto, 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=Visualizing+multiple+inter-organelle+contact+sites+using+the+organelle-+targeted+split-GFP+system.">Visualizing multiple inter-organelle contact sites using the organelle- targeted split-GFP system.</a> Sci Rep. 8 (1), 6175 (2018).</li><li>Wu, M. M., Covington, E. D., Lewis, R. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-molecule+analysis+of+diffusion+and+trapping+of+STIM1+and+Orai1+at+ER-plasma+membrane+junctions.">Single-molecule analysis of diffusion and trapping of STIM1 and Orai1 at ER-plasma membrane junctions.</a> Mol Biol Cell. 25 (22), (2014).</li><li>Csordas, 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=Structural+and+functional+features+and+significance+of+the+physical+linkage+between+ER+and+mitochondria.">Structural and functional features and significance of the physical linkage between ER and mitochondria.</a> J Cell Biol. 174 (7), 915-921 (2006).</li><li>de Brito, O. M., Scorrano, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitofusin+2+tethers+endoplasmic+reticulum+to+mitochondria.">Mitofusin 2 tethers endoplasmic reticulum to mitochondria.</a> Nature. 456 (7222), 605-610 (2008).</li><li>Kremer, 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=Developing+3D+SEM+in+a+broad+biological+context.">Developing 3D SEM in a broad biological context.</a> J Microsc. 259 (2), 80-96 (2015).</li><li>S&#246;derberg, O., 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=Direct+observation+of+individual+endogenous+protein+complexes+in+situ+by+proximity+ligation.">Direct observation of individual endogenous protein complexes in situ by proximity ligation.</a> Nat Methods. 3 (12), 995-1000 (2006).</li><li>Lim, Y., Cho, I. -. T., Rennke, H. G., Cho, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=&#946;2-adrenergic+receptor+regulates+ER-mitochondria+contacts.">&#946;2-adrenergic receptor regulates ER-mitochondria contacts.</a> Sci Rep. 11 (1), 21477 (2021).</li><li>Lam, S. S., 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=Directed+evolution+of+APEX2+for+electron+microscopy+and+proximity+labeling.">Directed evolution of APEX2 for electron microscopy and proximity labeling.</a> Nat Methods. 12 (1), 51-54 (2014).</li><li>Cho, I. -. T., 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=Ascorbate+peroxidase+proximity+labeling+coupled+with+biochemical+fractionation+identifies+promoters+of+endoplasmic+reticulum-mitochondrial+contacts.">Ascorbate peroxidase proximity labeling coupled with biochemical fractionation identifies promoters of endoplasmic reticulum-mitochondrial contacts.</a> J Biol Chem. 292 (39), 16382-16392 (2017).</li><li>Lim, Y., Cho, I. -. T., Schoel, L. J., Cho, G., Golden, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hereditary+spastic+paraplegia-linked+REEP1+modulates+endoplasmic+reticulum/mitochondria+contacts.">Hereditary spastic paraplegia-linked REEP1 modulates endoplasmic reticulum/mitochondria contacts.</a> Ann Neurol. 78 (5), 679-696 (2015).</li><li>Arnold, T. R., Stephenson, R. E., Miller, A. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rho+GTPases+and+actomyosin:+Partners+in+regulating+epithelial+cell-cell+junction+structure+and+function.">Rho GTPases and actomyosin: Partners in regulating epithelial cell-cell junction structure and function.</a> Exp Cell Res. 358 (1), 20-30 (2017).</li></ol>

The authors declare no conflicts of interest.

We have used a split-Renilla luciferase 8 reassembly assay (split-Rluc assay) to quantify the level of ER-mitochondria couplings. In this study, we have modified the original split-Rluc construct24 by generating a single vector, pCAG-MitoRlucN-T2A-RlucCER-IRES-mCherry, encoding each split-Rluc component (MitoRlucN and RlucCER) and a self-cleaving peptide 2A sequence from Thosea a...

The interactions between the ER and the mitochondria are vital for cellular homeostasis and survival1,2,3,4. Previous evidence indicates that any type of disruption or dysregulation in ER-mitochondria contact sites can contribute to several neurodegenerative, metabolic, and cardiovascular diseases, as well as cancer5,6,7,8,9,10. For example, an abnormal increase of Ca2+ uptake into the mitochondria can lead to cell death by opening mitochondria permeability transition pores, which are commonly seen in some models of Alzheimer&#39;s disease5,11. Similarly, reduced ER-mitochondria contacts can result in a decrease in ATP production&#160;and impairment of Ca2+ intake, as seen in models of amyotrophic lateral sclerosis5,11,12. As more studies are being conducted in the realm of ER-mitochondria contacts, additional disease-related proteins and genes that could affect these contacts are being discovered. Despite current knowledge and evidence showcasing the role of ER-mitochondria contact sites, much work is still needed to elucidate how these contacts could lead to loss of cellular function and ultimately cell death.
There have been various methods developed to evaluate the proximity of the two membranes, structural morphology, and the distance between the two organelle contact sites3,4,13. The approaches to monitor ER-mitochondria coupling include fluorescence marker-based imaging14,15, FRET-reporter-based imaging16, and split-fluorescence-probe-based imaging17,18, which use epifluorescence and confocal microscopy. Super-resolution and atomic resolution microscopy are also powerful tools for accurately visualizing inter-organelle contacts, although their utilization in contact site analysis is still limited since they require highly dedicated microscopes and technical expertise19. In addition, transmission electron microscopy (TEM), scanning electron microscopy (SEM), and other EM techniques such as electron tomography (ET) and cryo-electron microscopy, are commonly used as they provide high-resolution ultrastructural imaging of the contact sites, which are often impossible to explore using other experimental approaches20,21,22. However, these EM-based methods are a very low-throughput technique that can also be affected by chemical &#64257;xation procedures. More recently, proximity labeling-based methods have been used to detect contact sites as well as to identify new contact-site proteins. For example, proximity ligation assay (PLA) has been used to quantify organelle proximities23,24, while a revised version of the ascorbate peroxidase (APEX) assay has been utilized in identifying new contact-site proteins25,26. It is important to recognize that all these methods described above have strengths and intrinsic limitations in detecting the contacts between the organelles. Thus, the pairing of different techniques is required to obtain a thorough interpretation of the organelle contact sites.
Previously we have established the split-Renilla luciferase 8 reassembly assay (split-Rluc assay) to monitor the level of ER-mitochondria membrane contacts (Figure 1A)24,26,27. Briefly, each split half of Renilla luciferase is conjugated with an ER- or mitochondria- targeting sequence. When transfected together, each split half of the enzyme is expressed either in the ER or mitochondrial membrane. When the ER and mitochondria are positioned in close proximity to each other, the split halves come together and reconstitute the whole enzyme with luciferase activity. For the split-Rluc construct, we used Renilla luciferase 8 (Rluc8) in pBAD/Myc-His27 for the initial template. The split site (between amino acids 91 and 92) was determined based on previous reports27. For the N-terminal half of the Rluc8, DNA sequences for amino acids 1-91 of the Rluc8 were fused to the 3&#39; end of the FLAG tag and the mouse AKAP1 mitochondrial-targeting sequence in pcDNA3.1 TOPO vector by PCR27. For the C-terminal half targeted to the ER, DNA sequences that encode amino acids 92-311 were fused to the 5&#39; end of the myc tag and the yeast UBC6 ER localization sequence. Here, we have upgraded the split-Rluc plasmid construct such that split halves of the Renilla luciferase are expressed in a single vector (pCAG) under the same promoter and subsequently cleaved into two fragments as T2A, a self-cleaving peptide 2A sequence from Thosea asigna virus, is inserted in between the two split halves (Figure 1B). The plasmid DNA map and sequences are provided in Supplemental File 1 and Supplemental Figure S1. Using this system, we have measured the effects of three chemicals (inhibiting GTPases involved in actin polymerization) on ER-mitochondria contacts. This split-Rluc assay is a simple but robust assay system for high-throughput screening for inter-organelle contact modulators24.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1.7 mL SafeSeal Microcentrifuge Tube</td>
			<td>Sorenson</td>
			<td>16070</td>
			<td></td>
		</tr>
		<tr>
			<td>6-well plate TC Treated</td>
			<td>USA Scientific</td>
			<td>CC7682-7506</td>
			<td></td>
		</tr>
		<tr>
			<td>10 mL Pipette Tips OneTip</td>
			<td>USA Scientific</td>
			<td>1110-3700</td>
			<td></td>
		</tr>
		<tr>
			<td>10 &#956;L pipette tips OneTip</td>
			<td>USA Scientific</td>
			<td>1110-3700</td>
			<td></td>
		</tr>
		<tr>
			<td>20-200 &#956;L Beveled tips OneTip</td>
			<td>USA Scientific</td>
			<td>1111-1210</td>
			<td></td>
		</tr>
		<tr>
			<td>50 mL Polypropylene Conical Tube</td>
			<td>Falcon</td>
			<td>352070</td>
			<td></td>
		</tr>
		<tr>
			<td>96-Well Flipper Microtube Racks</td>
			<td>ThermoFisher Scientific</td>
			<td>8770-11</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well plate TC Treated&#160;</td>
			<td>USA Scientific</td>
			<td>CC7682-7596</td>
			<td></td>
		</tr>
		<tr>
			<td>100 mm x 20 mm TC Treated Dish</td>
			<td>USA Scientific</td>
			<td>CC7682-3394</td>
			<td></td>
		</tr>
		<tr>
			<td>1250 &#956;L Tips OneTip</td>
			<td>USA Scientific</td>
			<td>1112-1720</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge 5910&#160;Ri - Refrigerated Centrifuge</td>
			<td>Eppendorf</td>
			<td>5943000131</td>
			<td></td>
		</tr>
		<tr>
			<td>Dimethyl sulfoxide, anhydrous, &#8805;99.9%</td>
			<td>Sigma-Aldrich</td>
			<td>276855-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM, high glucose</td>
			<td>ThermoFisher Scientific</td>
			<td>11965092</td>
			<td></td>
		</tr>
		<tr>
			<td>DPBS, no calcium, no magnesium</td>
			<td>ThermoFisher Scientific</td>
			<td>14190144</td>
			<td></td>
		</tr>
		<tr>
			<td>EHop 016</td>
			<td>Bio-Techne Tocris</td>
			<td>6248</td>
			<td>Dissolve in DMSO; store at -70 &#176;C</td>
		</tr>
		<tr>
			<td>EnduRen Live Cell Substrate</td>
			<td>Promega</td>
			<td>E6481</td>
			<td>Store aliquots at -70 &#176;C</td>
		</tr>
		<tr>
			<td>Eppendorf 2-20 &#956;L pipette</td>
			<td>Eppendorf</td>
			<td>3123000039</td>
			<td></td>
		</tr>
		<tr>
			<td>Eppendorf Research plus 100-1000 &#956;L pipette</td>
			<td>Eppendorf</td>
			<td>3123000063</td>
			<td></td>
		</tr>
		<tr>
			<td>Eppendorf Research Plus 1-10 &#181;L pipette</td>
			<td>Eppendorf</td>
			<td>3123000020</td>
			<td></td>
		</tr>
		<tr>
			<td>Eppendorf Research plus 12-channel</td>
			<td>Eppendorf</td>
			<td>3125000028</td>
			<td></td>
		</tr>
		<tr>
			<td>Eppendorf Research plus 200 &#956;L pipette</td>
			<td>Eppendorf&#160;</td>
			<td>3123000055</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum, qualified, USDA-approved regions</td>
			<td>ThermoFisher Scientific</td>
			<td>10437028</td>
			<td></td>
		</tr>
		<tr>
			<td>Forma Steri-Cycle CO2&#160;Incubator, 184 L, Polished Stainless Steel</td>
			<td>ThermoFisher Scientific</td>
			<td>381</td>
			<td></td>
		</tr>
		<tr>
			<td>Hand tally counter</td>
			<td>Sigma-Aldrich</td>
			<td>HS6594</td>
			<td></td>
		</tr>
		<tr>
			<td>HEK 293T Cells</td>
			<td>ATCC</td>
			<td>CRL-3216</td>
			<td></td>
		</tr>
		<tr>
			<td>Hemacytometer - Neubauer Bright Line, Double-Counting Chamber</td>
			<td>LW Scientific</td>
			<td>CTL-HEMM-GLDR</td>
			<td></td>
		</tr>
		<tr>
			<td>Invitrogen TE Buffer</td>
			<td>ThermoFisher Scientific</td>
			<td>8019005</td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope</td>
			<td>Zeiss</td>
			<td>Axiovert 25 CFL</td>
			<td></td>
		</tr>
		<tr>
			<td>Mini centrifuge</td>
			<td>Benchmark Scientific</td>
			<td>C1012</td>
			<td></td>
		</tr>
		<tr>
			<td>Multi Tube Rack For 50ml Conical, 15ml Conical, And Microcentrifuge Tubes</td>
			<td>Boekel Scientific</td>
			<td>120008</td>
			<td></td>
		</tr>
		<tr>
			<td>PEI MAX - Transfection Grade Linear Polyethylenimine Hydrochloride (MW 40,000)</td>
			<td>Polysciences</td>
			<td>24765-100MG</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipet-Aid XP</td>
			<td>USA Scientific</td>
			<td>4440-0101</td>
			<td></td>
		</tr>
		<tr>
			<td>Poly-D-lysine hydrobromide</td>
			<td>Sigma-Aldrich</td>
			<td>P6407-5MG</td>
			<td></td>
		</tr>
		<tr>
			<td>Rhosin hydrochloride</td>
			<td>Bio-Techne Tocris</td>
			<td>5003</td>
			<td>Dissolve in DMSO; store at -70 &#176;C</td>
		</tr>
		<tr>
			<td>Trypsin-EDTA (0.05%), phenol red</td>
			<td>ThermoFisher Scientific</td>
			<td>25300054</td>
			<td></td>
		</tr>
		<tr>
			<td>Varioskan LUX multimode microplate reader</td>
			<td>ThermoFisher Scientific</td>
			<td>VL0000D0</td>
			<td></td>
		</tr>
		<tr>
			<td>Vortex</td>
			<td>ThermoFisher Scientific</td>
			<td>2215365</td>
			<td>level 8</td>
		</tr>
		<tr>
			<td>VWR Vacuum Aspiration System</td>
			<td>VWR</td>
			<td>75870-734</td>
			<td></td>
		</tr>
		<tr>
			<td>ZCL 278</td>
			<td>Bio-Techne Tocris</td>
			<td>4794</td>
			<td>Dissolve in DMSO; store at -70 &#176;C</td>
		</tr>
	</tbody>
</table>

split-luciferase reassembly assay to measure endoplasmic reticulum-mitochondria contacts in live cells

Endoplasmic reticulum (ER)-mitochondria contact sites play a critical role in cell health and homeostasis, such as the regulation of Ca2+ and lipid homeostasis, mitochondrial dynamics, autophagosome and mitophagosome biogenesis, and apoptosis. Failure to maintain normal ER-mitochondrial coupling is implicated in many neurodegenerative diseases such as Alzheimer&#39;s disease, Parkinson&#39;s disease, amyotrophic lateral sclerosis, and hereditary spastic paraplegia. It is of considerable significance to explore how the dysregulation of ER-mitochondrial contacts could lead to cell death and whether repairing these contacts to the normal level could ameliorate neurodegenerative conditions. Thus, improved assays that measure the level of these contacts could help to illuminate the pathogenic mechanisms of these diseases. Ultimately, establishing simple and reliable assays will facilitate the development of new therapeutic strategies. Here we describe&#160;a split-luciferase assay to quantitatively measure the level of ER-mitochondria contacts in live cells. This assay can be used to study the pathophysiological role of these contacts as well as to identify their modulators in high-throughput screening.

Author Spotlight: Regulation and Dysregulation of ER-Mitochondria Contacts &#8212; Implications for Neurodegenerative Disease Pathogenesis

Split-Luciferase Reassembly Assay to Measure Endoplasmic Reticulum-Mitochondria Contacts in Live Cells

In my lab, we study interorganal communication that takes a form of membrane contact and their roles in maintaining cellular health, as well as in disease pathogenesis. We're particularly interested in membrane contacts between mitochondria and endoplasmic reticulum and trying to understand how they're regulated and how their dysregulation can lead to neurodegeneration. Although we know that ER mitochondria contacts are important for cell health and their dysregulation is associated with many diseases, we do not know much about how their level is regulated.The first step to address this is to establish a simple, reliable protocol to measure the level of ER mitochondria contacts in cells. Our split luciferase assay offers an easier and faster way to quantify ER mitochondria contacts in live cells compared to most assays. We take advantage of two split halves of renilla luciferase, one half targeted to ER and the other to mitochondria.They can be reassembled together only where the ER and mitochondria membranes have close contact, which results in reconstituted luciferase with a full enzyme activity. This method is simple, suitable for high throughput screenings, and easily accessible for many labs. We hope that it will advance the neurodegenerative disease field by identifying molecular and genetic modulators of ER mitochondria contacts that can be further developed into therapeutic agents.Our results have paved the way for important questions such as how do different drugs or drug combinations affect ER mitochondria contacts, and what are the important molecular players behind these contacts. From these questions, we can gain a better understanding of the mechanism of ER mitochondria contacts, and find ways to combat related diseases.

We have used the protocol described above to measure the level of ER-mitochondria contacts upon the addition of three compounds known to inhibit specific GTPases. CDC42, RHO, and RAC are GTPases that promote actin polymerization28&#160;when activated&#160;and are inhibited by ZCL278, Rhosin, and Ehop-016, respectively24. HEK293T cells transfected with split-Rluc were treated with DMSO (control), ZCL278 (50 &#181;M), Rhosin (50 &#181;M), or Ehop-016 (25 &#181;M) and...

We have established a split-luciferase reassembly assay to monitor the endoplasmic reticulum-mitochondria contacts in live cells. Using this assay, we describe a protocol to quantitatively measure the level of these inter-organelle couplings in HEK293T cells, under the condition of chemical treatment.

Endoplasmic reticulum (ER)-mitochondria contact sites play a critical role in cell health and homeostasis, such as the regulation of Ca2+ and lipid ...

split-luciferase-reassembly-assay-to-measure-endoplasmic-reticulum

Research

JoVE Journal

Biochemistry

Maintaining and Seeding HEK293T Cells for Split-Rluc Plasmid Transfection

To begin, maintain HEK293T cells in culture media containing DMEM with 10%FBS in a humidified incubator. Check the plate's confluency under a microscope. When cells reach approximately 80 to 90%confluency, remove the media and wash them with 10 milliliters of DPBS.Then, remove the DPBS from the culture dish. Treat the cells with one milliliter of 0.05%trypsin-EDTA phenol red and incubate the cells for three minutes at 37 degrees Celsius. After removing the plate from the incubator, add nine milliliters of culture media to stop the trypsin reaction, and mix by pipetting to dislodge any remaining cells.Now, transfer the cell suspension to a 50-milliliter tube. Centrifuge at 300g for five minutes at room temperature. Once the media is removed, resuspend the cell pellets in one milliliter of fresh media.To plate cells in a six-well plate, combine the necessary volume of cells with 13 milliliters of media in a 50-milliliter tube. Then, dispense two milliliters of the diluted cell suspension into each of the six wells and gently tap the plate on all sides to spread the cells evenly. Afterward, place the plate in a humidified incubator at 37 degrees Celsius with 5%carbon dioxide overnight.

Polyethyleneimine (PEI)-Mediated HEK293T Cell Transfection and Post-Transfection Cell Seeding

To begin, take cultured HEK293T from the incubator. Aspirate out the existing culture media from each well, and add two milliliters of fresh media per well. For transfecting the cells with split R-loop plasmid DNA, mix the DNA and PEI in 200 microliters of DMEM in a 1.7-milliliter microcentrifuge tube for each well.Quickly vortex the DNA and PEI at level eight for approximately two seconds to ensure they mix well to form a complex. Then spin it down briefly in a mini centrifuge. After incubation, drop the mixture onto the surface of the culture media in the six well plate containing cells.Tap the plate gently to evenly distribute the mixture, and incubate it in a humidified incubator at 37 degrees Celsius with 5%carbon dioxide for six hours. Afterward, remove the six well plate from the incubator, aspirate out the media, and wash each well with two milliliters of DPBS. Once the DPBS is removed, add 350 microliters of 0.05%trypsin-EDTA phenol red.At the end of the incubation, add 1.7 milliliters of media to each well to stop the trypsin reaction. Now, transfer the cells along with media to a 50-milliliter tube, and spin at 300 G for five minutes in a tabletop centrifuge. Aspirate the media and resuspend the cell pellet with one milliliter of fresh media.To seed the cells in a poly-D-lysine coated 96 well plate, add the necessary volume of cells in a 50-milliliter tube along with the appropriate volume of media. Using a multichannel pipette, dispense 100 microliters of the diluted cell suspension into each of the 96 wells. Incubate the cells for 18 hours at 37 degrees Celsius with 5%carbon dioxide.

Chemical Treatment and Luciferase Assay to Measure the Level of ER-Mitochondria Contacts in Live Cells

To begin, seed split our loop transfected HEK293 T cells in a Poly-D-Lysine coated 96 well plate. Next, prepare three fresh solutions of Rhosin, Ehop-016, and ZCL278 in a 1.7 milliliter Microfuge II.Add live cell substrate for renilla luciferase, diluted 1 to 2, 000, to a final concentration of 30 millimolar to each solution. To make 0.55 and 50 micromolar ZCL278 solutions, perform serial dilutions using the initial 50 micromolar ZCL278 in culture media.Then remove the media from each well of the 96 well plate containing transfected cells. Add 50 microliters of the chemical and substrate media mixture to each well. After incubating the cells for one hour, two hours or five hours, load the plate onto the luminescence plate reader and measure luminescence.Ensure the plate reader is turned on before starting. Access the Microplate Reader Software and click new session to create a new file. Click incubator to set the plate reader's temperature to 37 degrees Celsius.Check the temperature option and type 37 degrees Celsius. Under plate layout, choose the option unknown and click and drag the well to specify the wells to measure. Then go to protocol, click luminescence, and keep the default settings.Once the setup is complete, load the plate with the lid off into the plate reader and choose run plate in. Click start and a save file window will appear. Rename the file and click save.Once the reading is complete, remove the plate from the plate reader and then click the run plate in option to put the reader back in. Once completed, place the plate back in the humidified incubator until the next reading. At one, two, and five hours of the treatment, Rhosin treated cells showed no significant changes in luciferase activity compared to control DMSO treated cells.The Rac GTPase Inhibitor EHop-016 showed significantly lower luciferase activity than DMSO. ZCL278 treated cells had significantly lower luciferase activity than the control DMSO at all three time points. Luciferase activities measured at one, two, and five hours post-treatment showed a dose-dependent response.Higher concentrations of ZCL278 still showed significant changes compared to the control DMSO.

1.3K Views.  Cedars-Sinai Medical Center.  We have established a split-luciferase reassembly assay to monitor the endoplasmic reticulum-mitochondria contacts in live cells. Using this assay, we describe a protocol to quantitatively measure the level of these inter-organelle couplings in HEK293T cells, under the condition of chemical treatment.

A Simple Assay to Measure ER-Mitochondria Contacts for High-Throughput Screens

Summary