Name: identifying inhibitors of the hbx-ddb1 interaction using a split luciferase assay system
Uploaded: 2019-12-21T14:00:00
Description: Watch this Scientific Journal Video about Identifying Inhibitors of the HBx-DDB1 Interaction Using a Split Luciferase Assay System at JoVE.com

This work was supported by Grants-in-Aid from the Ministry of Education, Culture, Sports, Science, and Technology, Japan (#19H03430 and #17K09405 to M.O., and #19J11829 to K.S.), by a Grant-in-Aid for Scientific Research on Innovative Areas (#18H05024 to M.O.), by the Research Program on Hepatitis from Japan Agency for Medical Research and Development, AMED (to M.O., #JP19fk021005), by program on the Innovative Development and the Application of New Drugs for Hepatitis B (#JP19fk0310102 to K.K.) from AMED, by grants from the Japan Foundation for Applied Enzymology and from the Kobayashi Foundation for Cancer Research (to M.O.), by GSK Japan Research Grant 2018 (to K.S.), and by a grant from the Miyakawa Memorial Research Foundation (to K.S.).

NOTE: A schematic representation of the split luciferase assay is shown in Figure 1A, and the assay process is outlined in Figure 1B. The interaction dynamics can be measured in real time without cell lysis.
1. Cell Preparation
<ol>
	<li>Maintain cultured HEK293T cells in Dulbecco&#39;s modified Eagle&#39;s medium (DMEM) supplemented with 10% v/v fetal bovine serum (FBS), 1x penicil...

<ol>
	<li>Tang, L. S. Y., Covert, E., Wilson, E., Kottilil, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chronic+hepatitis+B+infection:+a+review.">Chronic hepatitis B infection: a review.</a> The Journal of the American Medical Association. 319, 1802-1813 (2018).</li><li>Sekiba, K., 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=Hepatitis+B+virus+pathogenesis:+Fresh+insights+into+hepatitis+B+virus+RNA.">Hepatitis B virus pathogenesis: Fresh insights into hepatitis B virus RNA.</a> World Journal of Gastroenterology. 24, 2261-2268 (2018).</li><li>Slagle, B. L., Bouchard, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hepatitis+B+virus+X+and+regulation+of+viral+gene+expression.">Hepatitis B virus X and regulation of viral gene expression.</a> Cold Spring Harbor Perspectives in Medicine. 6, a021402 (2016).</li><li>Murphy, C. 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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=NanoLuc+Complementation+Reporter+Optimized+for+Accurate+Measurement+of+Protein+Interactions+in+Cells.">NanoLuc Complementation Reporter Optimized for Accurate Measurement of Protein Interactions in Cells.</a> ACS Chemical Biology. 11, 400-408 (2015).</li><li>Zhang, J. H., Chung, T. D. Y., Oldenburg, K. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+simple+statistical+parameter+for+use+in+evaluation+and+validation+of+high+throughput+screening+assays.">A simple statistical parameter for use in evaluation and validation of high throughput screening assays.</a> Journal of Biomolecular Screening. 4, 67-73 (1999).</li><li>Rao, V. S., Srinivas, K., Sujini, G. N., Kumar, G. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein-protein+interaction+detection:+Methods+and+analysis.">Protein-protein interaction detection: Methods and analysis.</a> International Journal of Proteomics. 2014. 2014, 147648 (2014).</li><li>Michael, 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=A+Robotic+Platform+for+Quantitative+High-Throughput+Screening.">A Robotic Platform for Quantitative High-Throughput Screening.</a> ASSAY and Drug Development Technologies. 6, 637-657 (2008).</li><li>Skwarczynska, M., Ottmann, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein-protein+interactions+as+drug+targets.">Protein-protein interactions as drug targets.</a> Future Medicinal Chemistry. 7, 2195-2219 (2015).</li><li>de Chassey, B., Meyniel-Schicklin, L., Vonderscher, J., Andr&#233;, P., Lotteau, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Virus-host+interactomics:+New+insights+and+opportunities+for+antiviral+drug+discovery.">Virus-host interactomics: New insights and opportunities for antiviral drug discovery.</a> Genome Medicine. 6, 115 (2014).</li><li>Prasad, 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=Virus-Host+Interactions:+New+Insights+and+Advances+in+Drug+Development+Against+Viral+Pathogens.">Virus-Host Interactions: New Insights and Advances in Drug Development Against Viral Pathogens.</a> Current Drug Metabolism. 18, 942-970 (2017).</li></ol>

We developed a convenient screening method using a split luciferase assay to find HBx-DDB1 binding inhibitors. The interaction dynamics can be detected in real time in living cells without the need for cell lysis. Inhibition of the HBx-DDB1 interaction leads to restoration of Smc5/6, which results in suppression of viral transcription, protein expression, and cccDNA production7. This novel mechanism of antiviral action may overcome the inadequacies of current HBV therapies.
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Hepatitis B virus (HBV) infection is a major public health concern worldwide, with annual estimates of 240 million people chronically infected with HBV and 90,000 deaths due to complications from the infection, including cirrhosis and hepatocellular carcinoma (HCC)1. Although the current anti-HBV therapeutic agents, nucleos(t)ide analogues, sufficiently inhibit viral reverse transcription, they rarely achieve elimination of viral proteins, which is the long-term clinical goal. Their poor effect on viral protein elimination is due to their lack of direct effect on viral transcription from episomal viral covalently closed circular DNA (cccDNA) minichromosomes in the hepatocyte nucleus2.
HBV transcription is activated by HBV regulatory X (HBx) protein3. Recent studies revealed that HBx degrades structural maintenance of chromosomes 5/6 (Smc5/6), a host restriction factor that blocks HBV transcription from cccDNA, via hijacking a DDB1-CUL4-ROC1 E3 ubiquitin ligase complex4,5,6. Therefore, a crucial step in promoting viral transcription from cccDNA is thought to be the HBx-DDB1 interaction. Compounds capable of inhibiting the binding between HBx and DDB1 may block viral transcription, and indeed nitazoxanide was identified as an inhibitor of the HBx-DDB1 interaction via a screening system developed in our laboratory7.
Here, we present our convenient screening system used to identify inhibitors of the HBx-DDB1 interaction, which utilizes a split luciferase complementary assay7,8. Split luciferase subunits are fused to HBx and DDB1, and the HBx-DDB1 interaction brings the subunits into close proximity to form a functional enzyme that generates a bright luminescent signal. As the interaction between the subunits is reversible, this system can detect rapidly dissociating HBx-DDB1 proteins (Figure 1). Using this system, a large compound library can be easily screened, which may result in the discovery of novel compounds capable of efficiently inhibiting the HBx-DDB1 interaction.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Cell culture microplate, 96 well, PS, F-BOTTOM</td>
			<td>Greiner-Bio-One GmbH</td>
			<td>655098</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Sigma Aldrich</td>
			<td>D6046</td>
			<td></td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Tocris Bioscience</td>
			<td>3176</td>
			<td></td>
		</tr>
		<tr>
			<td>Effectene transfection reagent</td>
			<td>Qiagen</td>
			<td>301425</td>
			<td>Includes DNA-condensation buffer, enhancer solution and transfection reagent</td>
		</tr>
		<tr>
			<td>FBS</td>
			<td>Nichirei</td>
			<td>175012</td>
			<td></td>
		</tr>
		<tr>
			<td>GloMax 96 microplate luminometer</td>
			<td>Promega</td>
			<td>E6521</td>
			<td></td>
		</tr>
		<tr>
			<td>HBx&#8211;LgBit expressing DNA plasmid</td>
			<td>Our laboratory</td>
			<td></td>
			<td>Available upon request</td>
		</tr>
		<tr>
			<td>HEK293T cells</td>
			<td>American Type Culture Collection</td>
			<td>CRL-11268</td>
			<td></td>
		</tr>
		<tr>
			<td>NanoBiT PPI starter systems</td>
			<td>Promega</td>
			<td>N2015</td>
			<td>Includes Nano-Glo Live Cell Reagent</td>
		</tr>
		<tr>
			<td>Opti-MEM</td>
			<td>Thermo Fisher Scientific</td>
			<td>11058021</td>
			<td>Described as &#34;buffered cell culture medium&#34; in the manuscript</td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Takara</td>
			<td>T900</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>Sigma Aldrich</td>
			<td>P0781</td>
			<td></td>
		</tr>
		<tr>
			<td>Screen-Well FDA-approved drug library V2 version 1.0</td>
			<td>Enzo Life Sciences</td>
			<td>BML-2841</td>
			<td>Compounds used here were as follows: mequinol, mercaptopurine hydrate, mesna, mestranol, metaproterenol hemisulfate, metaraminol bitartrate, metaxalone, methacholine chloride, methazolamide, methenamine hippurate, methocarbamol, methotrexate, methoxsalen, methscopolamine bromide, methsuximide, methyclothiazide, methyl aminolevulinate&#183;HCl, methylergonovine maleate, metolazone, metyrapone, mexiletine&#183;HCl, micafungin, miconazole, midodrine&#183;HCl, miglitol, milnacipran&#183;HCl, mirtazapine, mitotane, moexipril&#183;HCl, mometasone furoate, mupirocin, nadolol, nafcillin&#183;Na, naftifine&#183;HCl, naratriptan&#183;HCl, natamycin, nebivolol&#183;HCl, nelarabine, nepafenac, nevirapine, niacin, nicotine, nilotinib, nilutamide, nitazoxanide, nitisinone, nitrofurantoin, nizatidine, nortriptyline&#183;HCl, olsalazine&#183;Na, orlistat, oxaprozin, oxtriphylline, oxybutynin Chloride, oxytetracycline&#183;HCl, paliperidone, palonosetron&#183;HCl, paromomycin sulfate, pazopanib&#183;HCl, pemetrexed disodium, pemirolast potassium, penicillamine, penicillin G potassium, pentamidine isethionate, pentostatin, perindopril erbumine, permethrin, perphenazine, phenelzine sulfate, phenylephrine, phytonadione, pimecrolimus, pitavastatin calcium, and podofilox</td>
		</tr>
		<tr>
			<td>SmBit&#8211;DDB1 expressing DNA plasmid</td>
			<td>Our laboratory</td>
			<td></td>
			<td>Available upon request</td>
		</tr>
		<tr>
			<td>Trypsin-EDTA</td>
			<td>Sigma Aldrich</td>
			<td>T4049</td>
			<td></td>
		</tr>
	</tbody>
</table>

identifying inhibitors of the hbx-ddb1 interaction using a split luciferase assay system

There is an urgent need for novel therapeutic agents for hepatitis B virus (HBV) infection. Although currently available nucleos(t)ide analogs potently inhibit viral replication, they have no direct effect on the expression of viral proteins transcribed from a viral covalently closed circular DNA (cccDNA). As high viral antigen load may play a role in this chronic and HBV-related carcinogenesis, the goal of HBV treatment is to eradicate viral proteins. HBV regulatory protein X (HBx) binds to the host DNA damage-binding protein 1 (DDB1) protein to degrade structural maintenance of chromosomes 5/6 (Smc5/6), resulting in activation of viral transcription from cccDNA. Here, using a split luciferase complementation assay system, we present a comprehensive compound screening system to identify inhibitors of the HBx-DDB1 interaction. Our protocol enables easy detection of interaction dynamics in real time within living cells. This technique may become a key assay to discover novel therapeutic agents for treatment of HBV infection.

Representative outcomes following the use of this protocol are shown in Figure 2A,B. The signal-to-background ratio was greater than 80 and the Z&#39; factor9 (the gold standard quality index for high-throughput screening) was greater than 0.5, indicating that this assay system was acceptable for high-throughput screening. With the threshold set to &#62;40% inhibition compared with the control (DMSO only), we identifie...

Watch this Scientific Journal Video about Identifying Inhibitors of the HBx-DDB1 Interaction Using a Split Luciferase Assay System at JoVE.com

Identifying Inhibitors of the HBx-DDB1 Interaction Using a Split Luciferase Assay System

Here, we present a method for screening anti-hepatitis B viral agents that inhibit the HBx-DDB1 interaction using a split luciferase assay system. This system allows easy detection of protein-protein interactions and is suitable for identifying inhibitors of such interactions.

There is an urgent need for novel therapeutic agents for hepatitis B virus (HBV) infection. Although currently available nucleos(t)ide analogs potently ...

The HBX-DDB1 interaction is a crucial step for promoting HPV transcription from cccDNA, so this protocol may become a key asset to discover novel therapeutic agents for HPV functional cure. Our procedure is simple and requires only a short time to screen. The interaction that I mix can be detected in real-time without requiring cell lysis.Moreover, the screening quality is satisfactory with a high Z prime score. Inhibition of the HBX-DDB1 interaction leads to restoration of Smc5/6, which results in suppression of HPV transcription, protein expression, and cccDNA production. This novel mechanism of antiviral action may overcome the inadequacies of current HPV therapies.Protein-protein interactions are important class of drug targets. The split-luciferase-based acid described here, which targets the interactions between viral and hasS proteins, may provide a new strategy to develop cures for other infectious diseases. Although our protocol is simple and easy to understand, some steps may be hard to reproduce without the visual demonstration.Thus, the visual demonstration will be a great help to understand our protocol. Begin by seeding five times 10 to the 5th HEK293T cells into a 100 millimeter dish with 10 milliliters of DMEM, and incubating them overnight at 37 degrees celsius. On the next day, dilute one microgram each of HBx-LgBit and SmBit-DDB1 expressing DNA plasmids and DNA condensation buffer for a total volume of 300 microliters.Add 16 microliters of enhancer solution, and mix the tubes by vortexing for one second. Incubate the sample at room temperature for three minutes, then add 60 microliters of transfection reagent. Vortex the tube for 10 seconds, and incubate the sample for another eight minutes.Meanwhile, aspirate the medium from the dish with the cells and wash them with five milliliters of PVS. Aspirate the PVS and add seven milliliters of DMEM. Add three milliliters of DMEM to the tube with the transfection complexes, pipette up and down to mix, and add the mixture to the cells.Then, incubate the cells at 37 degrees celsius and five percent carbon dioxide for 10 hours. After the incubation, remove the spent culture medium, and wash the cells with five milliliters of PVS. Remove the PVS at one milliliter of 0.25%trypsin EDTA, and incubate the cells at 37 degrees celsius to detach them.Next, add four milliliters of DMEM, and disperse the medium by pipetting it over the surface of the cell layer several times, and transfer the suspension to a tube. Centrifuge the cells at 500 times G for five minutes, then discard the supernatant, and re-suspend the cell pellet in one milliliter of PVS. Repeat the cetrifugation and discard the supernatant.Then, re-suspend the cell pellet with buffered cell culture medium supplemented with 10%FBS to a seeding density of one million cells per milliliter. Pipette 50 microliters of the cell suspension into each well of a 96-well plate, and return the cells to the 37-degree-celsius incubator for 10 hours. While the cells are incubating, dilute the screening compounds and solvent to 13.5 X concentration.Add 12.5 microliters of luminescent substrate to each well, and incubate the plate for five minutes at room temperature. Measure the baseline luminescence with a luminometer, and add five microliters of the compounds and controlled DMSO to each well immediately after. Measure luminescence every 30 minutes for two hours, then calculate the inhibitory effects of the compounds in comparison with DMSO treatment.Baseline luminescence signals were measured, and the signal-to-background ratio was calculated to be greater than 80. The Z prime was greater than 0.5, indicating that this assay system is acceptable for high-throughput screening. By setting the threshold to greater than 40%inhibition compared to the DMSO-only control, nitazoxanide was identified as a candidate drug.We previously identified nitazoxanide as an inhibitor of the HBX-DDB1 interaction by screening a reactivity small-scale compound library with this method. Using nitazoxanide, we confirm that inhibition of the HBX-DDB1 interaction, that reduction of viral transcription, and subsequent viral product levels. The optimal portion of the split luciferase fused to a target protein must be determined beforehand.In this case, HPX fused to Large Bit at the C terminus of HPX and DDB1 fused to Small Bit at the end terminus of DDB1 provided the best results.

identifying-inhibitors-hbx-ddb1-interaction-using-split-luciferase

Research

JoVE Journal

Medicine

Experimental Generation of Carcinoma-Associated Fibroblasts (CAFs) from Human Mammary Fibroblasts

Carcinomas are complex tissues comprised of neoplastic cells and a non-cancerous compartment referred to as the 'stroma'. The stroma consists of extracellular matrix (ECM) and a variety of mesenchymal cells, including fibroblasts, myofibroblasts, endothelial cells, pericytes and leukocytes 1-3.
The tumour-associated stroma is responsive to substantial paracrine signals released by neighbouring carcinoma cells. During the disease process, the stroma often becomes populated by carcinoma-associated fibroblasts (CAFs) including large numbers of myofibroblasts. These cells have previously been extracted from many different types of human carcinomas for their in vitro culture. A subpopulation of CAFs is distinguishable through their up-regulation of &alpha;-smooth muscle actin (&alpha;-SMA) expression4,5. These cells are a hallmark of 'activated fibroblasts' that share similar properties with myofibroblasts commonly observed in injured and fibrotic tissues 6. The presence of this myofibroblastic CAF subset is highly related to high-grade malignancies and associated with poor prognoses in patients.
Many laboratories, including our own, have shown that CAFs, when injected with carcinoma cells into immunodeficient mice, are capable of substantially promoting tumourigenesis 7-10. CAFs prepared from carcinoma patients, however, frequently undergo senescence during propagation in culture limiting the extensiveness of their use throughout ongoing experimentation. To overcome this difficulty, we developed a novel technique to experimentally generate immortalised human mammary CAF cell lines (exp-CAFs) from human mammary fibroblasts, using a coimplantation breast tumour xenograft model.
In order to generate exp-CAFs, parental human mammary fibroblasts, obtained from the reduction mammoplasty tissue, were first immortalised with hTERT, the catalytic subunit of the telomerase holoenzyme, and engineered to express GFP and a puromycin resistance gene. These cells were coimplanted with MCF-7 human breast carcinoma cells expressing an activated ras oncogene (MCF-7-ras cells) into a mouse xenograft. After a period of incubation in vivo, the initially injected human mammary fibroblasts were extracted from the tumour xenografts on the basis of their puromycin resistance 11.
We observed that the resident human mammary fibroblasts have differentiated, adopting a myofibroblastic phenotype and acquired tumour-promoting properties during the course of tumour progression. Importantly, these cells, defined as exp-CAFs, closely mimic the tumour-promoting myofibroblastic phenotype of CAFs isolated from breast carcinomas dissected from patients. Our tumour xenograft-derived exp-CAFs therefore provide an effective model to study the biology of CAFs in human breast carcinomas. The described protocol may also be extended for generating and characterising various CAF populations derived from other types of human carcinomas.

Experimental Generation of Carcinoma-Associated Fibroblasts CAFs from Human Mammary Fibroblasts

Carcinoma-associated fibroblasts (CAFs) rich in myofibroblasts present within the tumour stroma, play a major role in driving tumour progression. We developed a coimplantation tumour xengraft model for experimentally generating CAFs from human mammary fibroblasts. The protocol describes how to establish CAF myofibroblasts that acquire an ability to promote tumourigenesis.

Carcinomas are complex tissues comprised of neoplastic cells and a non-cancerous compartment referred to as the 'stroma'. The stroma consists of ...

Intraoperative Detection of Subtle Endometriosis: A Novel Paradigm for Detection and Treatment of Pelvic Pain Associated with the Loss of Peritoneal Integrity

Endometriosis is a common disease affecting 40 to 70% of reproductive-aged women with chronic pelvic pain (CPP) and/or infertility. The purpose of this study was to demonstrate the use of a blue dye (methylene blue) to stain peritoneal surfaces during laparoscopy (L/S) to detect the loss of peritoneal integrity in patients with pelvic pain and suspected endometriosis. Forty women with CPP and 5 women without pain were evaluated in this pilot study. During L/S, concentrated dye was sprayed onto peritoneal surfaces, then aspirated and rinsed with Lactated Ringers solution. Areas of localized dye uptake were evaluated for the presence of visible endometriotic lesions. Areas of intense peritoneal staining were resected and some fixed in 2.5% buffered gluteraldehyde and examined by scanning (SEM) electron microscopy. Blue dye uptake was more common in women with endometriosis and chronic pelvic pain than controls (85% vs. 40%). Resection of the blue stained areas revealed endometriosis by SEM and loss of peritoneal cell-cell contact compared to normal, non-staining peritoneum. Affected peritoneum was associated with visible endometriotic implants in most but not all patients. Subjective pain relief was reported in 80% of subjects. Based on scanning electron microscopy, we conclude that endometrial cells extend well beyond visible implants of endometriosis and appear to disrupt the underlying mesothelium. Subtle lesions of endometriosis could therefore cause pelvic pain by disruption of peritoneal integrity, allowing menstrual or ovulatory blood and associated pain factors access to underlying sensory nerves. Complete resection of affected peritoneum may provide a better long-term treatment for endometriosis and CPP. This simple technique appears to improve detection of subtle or near invisible endometriosis in women with CPP and minimal visual findings at L/S and may serve to elevate diagnostic accuracy for endometriosis at laparoscopy.

Loss of peritoneal integrity provides a new paradigm to understand and treat chronic pelvic pain in women with mild forms of endometriosis and can be easily detected using intraoperative instillation of dye at the time of laparoscopy.

Endometriosis is a  common disease affecting 40 to 70% of reproductive-aged women with chronic  pelvic pain (CPP) and/or infertility. The purpose of this ...

Three-Dimensional (3D) Tumor Spheroid Invasion Assay

Invasion of surrounding normal tissues is generally considered to be a key hallmark of malignant (as opposed to benign) tumors. For some cancers in particular (e.g., brain tumors such as glioblastoma multiforme and squamous cell carcinoma of the head and neck &#8211; SCCHN) it is a cause of severe morbidity and can be life-threatening even in the absence of distant metastases. In addition, cancers which have relapsed following treatment unfortunately often present with a more aggressive phenotype. Therefore, there is an opportunity to target the process of invasion to provide novel therapies that could be complementary to standard anti-proliferative agents. Until now, this strategy has been hampered by the lack of robust, reproducible assays suitable for a detailed analysis of invasion and for drug screening. Here we provide a simple micro-plate method (based on uniform, self-assembling 3D tumor spheroids) which has great potential for such studies. We exemplify the assay platform using a human glioblastoma cell line and also an SCCHN model where the development of resistance against targeted epidermal growth factor receptor (EGFR) inhibitors is associated with enhanced matrix-invasive potential. We also provide two alternative methods of semi-automated quantification: one using an imaging cytometer and a second which simply requires standard microscopy and image capture with digital image analysis.

Three-Dimensional 3D Tumor Spheroid Invasion Assay

Invasion of surrounding normal tissues is a defining characteristic of malignant tumors. We provide here a simple, semi-automated micro-plate assay of invasion into a natural 3D biomatrix that has been exemplified with a number of models of advanced human cancers.

Invasion of surrounding normal tissues is generally considered to be a key hallmark of malignant (as opposed to benign) tumors. For some cancers in ...

Utilization of the Soft Agar Colony Formation Assay to Identify Inhibitors of Tumorigenicity in Breast Cancer Cells

Given the inherent difficulties in investigating the mechanisms of tumor progression in vivo, cell-based assays such as the soft agar colony formation assay (hereafter called soft agar assay), which measures the ability of cells to proliferate in semi-solid matrices, remain a hallmark of cancer research. A key advantage of this technique over conventional 2D monolayer or 3D spheroid cell culture assays is the close mimicry of the 3D cellular environment to that seen in vivo. Importantly, the soft agar assay also provides an ideal tool to rigorously test the effects of novel compounds or treatment conditions on cell proliferation and migration. Additionally, this assay enables the quantitative assessment of cell transformation potential within the context of genetic perturbations. We recently identified peptidylarginine deiminase 2 (PADI2) as a potential breast cancer biomarker and therapeutic target. Here we highlight the utility of the soft agar assay for preclinical anti-cancer studies by testing the effects of the PADI inhibitor, BB-Cl-amidine (BB-CLA), on the tumorigenicity of human ductal carcinoma in situ (MCF10DCIS) cells.

Here, we document the use of the soft agar colony formation assay to test the effects of a peptidylarginine deiminase (PADI) enzyme inhibitor, BB-Cl-amidine, on breast cancer tumorigenicity in vitro.

Given the inherent difficulties in investigating the mechanisms of tumor progression in vivo, cell-based assays such as the soft agar colony formation ...

Drug Repurposing Hypothesis Generation Using the "RE:fine Drugs" System

The promise of drug repurposing is that existing drugs may be used for new disease indications in order to curb the high costs and time for approval. The goal of computational methods for drug repurposing is to enable solutions for safer, cheaper and faster drug discovery. Towards this end, we developed a novel method that integrates genetic and clinical phenotype data from large-scale GWAS and PheWAS studies with detailed drug information on the concept of transitive Drug-Gene-Disease triads. We created "RE:fine Drugs," a freely available, interactive dashboard that automates gene, disease and drug-based searches to identify drug repurposing candidates. This web-based tool supports a user-friendly interface that includes an array of advanced search and export options. Results can be prioritized in a variety of ways, including but not limited to, biomedical literature support, strength and statistical significance of GWAS and/or PheWAS associations, disease indications and molecular drug targets. Here we provide a protocol that illustrates the functionalities available in the "RE:fine Drugs" system and explores the different advanced options through a case study.

Drug Repurposing Hypothesis Generation Using the &quot;RE:fine Drugs&quot; System

Here we describe a protocol using the web-based drug repurposing hypothesis generation tool: "RE:fine Drugs." This protocol can be modified to a user's preferences at the level of the query type (gene, drug or disease) and/or the range of available advanced options.

The promise of drug repurposing is that existing drugs may be used for new disease indications in order to curb the high costs and time for approval. The ...

Identifying Coronary Artery Calcification on Non-gated Computed Tomography Scans

Coronary artery calcification (CAC) provides an objective measure of coronary artery disease and can readily be identified on non-gated computed tomography (CT) scans with a high correlation with gated cardiac CT scans. This standardized protocol takes a step-wise approach to not only optimizing an image for the identification of calcification but also to distinguishing CAC from other common causes of calcification in the cardiac silhouette. Recognition of CAC on non-gated CT scans helps to identify a very powerful prognostic factor that can influence therapeutic interventions or downstream diagnostic testing without requiring a gated cardiac scan. These non-gated CT scans are often acquired as part of the routine care of the patient, and this data is readily available without another dose of&#160;ionizing radiation. This protocol allows for the precise and accurate extraction of this data for the purposes of retrospective data analysis in clinical research studies, but also in the clinical evaluation and management of patients.

Here, we present a protocol to reliably and systematically identify coronary artery calcification (CAC) on non-gated computed tomography (CT) scans of the chest or abdomen. CAC provides an objective measure of coronary artery disease for both research and clinical purposes.

Coronary artery calcification (CAC) provides an objective measure of coronary artery disease and can readily be identified on non-gated computed ...

Visualization of Endogenous Mitophagy Complexes In Situ in Human Pancreatic Beta Cells Utilizing Proximity Ligation Assay

Mitophagy is an essential mitochondrial quality control pathway, which is crucial for pancreatic islet beta cell bioenergetics to fuel glucose-stimulated insulin release. Assessment of mitophagy is challenging and often requires genetic reporters or multiple complementary techniques not easily utilized in tissue samples, such as primary human pancreatic islets. Here we demonstrate a robust approach to visualize and quantify formation of key endogenous mitophagy complexes in primary human pancreatic islets. Utilizing the sensitive proximity ligation assay technique to detect interaction of the mitophagy regulators NRDP1 and USP8, we are able to specifically quantify formation of essential mitophagy complexes in situ. By coupling this approach to counterstaining for the transcription factor PDX1, we can quantify mitophagy complexes, and the factors that can impair mitophagy, specifically within beta cells. The methodology we describe overcomes the need for large quantities of cellular extracts required for other protein-protein interaction studies, such as immunoprecipitation (IP) or mass spectrometry, and is ideal for precious human islet&#160;samples generally not available in sufficient quantities for these approaches. Further, this methodology obviates the need for flow sorting techniques to purify beta cells from a heterogeneous islet population for downstream protein applications. Thus, we describe a valuable protocol for visualization of mitophagy highly compatible for use in heterogeneous and limited cell populations.

This protocol outlines a method for quantitative analysis of mitophagy protein complex formation specifically in beta cells from primary human islet samples. This technique thus allows analysis of mitophagy from limited biological material, which are crucial in precious human pancreatic beta cell samples.

Mitophagy is an essential mitochondrial quality control pathway, which is crucial for pancreatic islet beta cell bioenergetics to fuel glucose-stimulated ...

A Porcine Corneal Endothelial Organ Culture Model Using Split Corneal Buttons

Experimental research on corneal endothelial cells is associated with several difficulties. Human donor corneas are scarce and rarely available for experimental investigations as they are normally needed for transplantation. Endothelial cell cultures often do not translate well to in vivo situations. Due to the biostructural characteristics of non-human corneas, stromal swelling during cultivation induces substantial corneal endothelial cell loss, which makes it difficult to perform cultivation for an extended period of time. Deswelling agents such as dextran are used to counteract this response. However, they also cause significant endothelial cell loss. Therefore, an ex vivo organ culture model not requiring deswelling agents was established. Pig eyes from a local slaughterhouse were used to prepare split corneal buttons. After partial corneal trephination, the outer layers of the cornea (epithelium, bowman layer, parts of the stroma) were removed. This significantly reduces corneal endothelial cell loss induced by massive stromal swelling and Descemet&#39;s membrane folding throughout longer cultivation periods and improves general preservation of the endothelial cell layer. Subsequent complete corneal trephination was followed by the removal of the split corneal button from the remaining eye bulb and cultivation. Endothelial cell density was assessed at follow-up times of up to 15 days after preparation (i.e., days 1, 8, 15) using light microscopy. The preparation technique used allows a better preservation of the endothelial cell layer enabled by less stromal tissue swelling, which results in slow and linear decline rates in split corneal buttons comparable to human donor corneas. As this standardized organo-typically cultivated research model for the first time allows a stable cultivation for at least two weeks, it is a valuable alternative to human donor corneas for future investigations of various external factors with regards to their effects on the corneal endothelium.

Here, a step-by-step protocol for the preparation and cultivation of porcine split corneal buttons is presented. As this organo-typically cultivated organ culture model shows cell death rates within 15 days, comparable to human donor corneas, it represents the first model allowing long-term cultivation of non-human corneas without adding toxic dextran.

Experimental research on corneal endothelial cells is associated with several difficulties. Human donor corneas are scarce and rarely available for ...

Laminectomy for the Removal of Thoracic Ossification of the Ligamentum Flavum (TOLF) Using Ultrasonic and Conventional Osteotomes

Thoracic ossification of the ligamentum flavum (TOLF) is a common cause of progressive thoracic myelopathy. TOLF is typically treated with surgical decompression. A variety of surgical techniques, including laminoplasty, laminectomy, and lamina fenestration, are used for the effective treatment of TOLF. However, traditional methods are associated with a substantial risk of perioperative complications, including dural laceration and/or iatrogenic spinal cord injury. Therefore, it is important to develop an efficient and secure surgical technique for TOLF. Herein, we describe a method for laminectomyperformed at the thoracic spine using an ultrasonic osteotome combined with a conventional osteotome. This technique can reduce intraoperative complications. This is a relatively safe and easy-to-learn method that should be recommended for the treatment of TOLF.

Laminectomy for the Removal of Thoracic Ossification of the Ligamentum Flavum TOLF Using Ultrasonic and Conventional Osteotomes

We present a methodology for using an ultrasonic osteotome combined with a conventional osteotome for laminectomy in thoracic ossification of the ligamentum flavum. This is a relatively safe and easy-to-learn method that avoids the perioperative complications associated with the conventional method.

Thoracic ossification of the ligamentum flavum (TOLF) is a common cause of progressive thoracic myelopathy. TOLF is typically treated with surgical ...

Enhancing Stroke Rehabilitation with Virtual Reality-Based Occupational Training

Cognitive Function and Upper Limb Rehabilitation Training Post-Stroke Using a Digital Occupational Training System

Stroke rehabilitation often requires frequent and intensive therapy to improve functional recovery. Virtual reality (VR) technology has shown the potential to meet these demands by providing engaging and motivating therapy options. The digital occupational training system is a VR application that utilizes cutting-edge technologies, including multi-touch screens, virtual reality, and human-computer interaction, to offer diverse training techniques for advanced cognitive capacity and hand-eye coordination abilities. The objective of this study was to assess the effectiveness of this program in enhancing cognitive function and upper extremity rehabilitation in stroke patients. The training and assessment consist of five cognitive modules covering perception, attention, memory, logical reasoning, and calculation, along with hand-eye coordination training. This research indicates that after eight weeks of training, the digital occupational training system can significantly improve cognitive function, daily living skills, attention, and self-care abilities in stroke patients. This software can be employed as a time-saving and clinically effective rehabilitation aid to complement traditional one-on-one occupational therapy sessions. In summary, the digital occupational training system shows promise and offers potential financial benefits as a tool to support the functional recovery of stroke patients.

Author Spotlight: Rehabilitation of Stroke Patients With a Digital Occupational Training System

The current protocol outlines how the VR-based digital occupational training system enhances the rehabilitation of patients with cognitive impairment and upper limb dysfunction following a stroke.