Name: toxicity screens in human retinal organoids for pharmaceutical discovery
Uploaded: 2021-03-04T15:00:00
Description: Watch this Scientific Journal Video about Toxicity Screens in Human Retinal Organoids for Pharmaceutical Discovery at JoVE.com

Supported by the Lowy Medical Research Institute. We would like to thank the Lowy family for their support of the MacTel project. We would like to thank Mari Gantner, Mike Dorrell, and Lea Scheppke for their intellectual input and assistance preparing the manuscript.

1. Thawing, passaging, and expanding iPSCs/ESCs
NOTE: For all cell culturing steps, use best practices to maintain a sterile cell culture.
<ol>
	<li>Coat a 6-well cell culture plate with basement membrane matrix medium.
	<ol>
		<li>To prepare 1x of this medium, follow product specifications or dilute 75 &#181;L cold matrix medium with 9 mL of DMEM/F12. Add 1.5 mL of freshly prepared 1x medium per well in a 6-well plate. Incubate at 37 &#176;C for 30 min.</li>
		<li>Aspirate off the basement ...

<ol>
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J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Engineered+tissues+and+strategies+to+overcome+challenges+in+drug+development.">Engineered tissues and strategies to overcome challenges in drug development.</a> Advances in Drug Delivery Reviews. 158, 116-139 (2020).</li><li>Demetrius, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Of+mice+and+men.+When+it+comes+to+studying+ageing+and+the+means+to+slow+it+down,+mice+are+not+just+small+humans.">Of mice and men. When it comes to studying ageing and the means to slow it down, mice are not just small humans.</a> EMBO Reports. , 39-44 (2005).</li><li>Lindsay, K. 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=Pyruvate+kinase+and+aspartate-glutamate+carrier+distributions+reveal+key+metabolic+links+between+neurons+and+glia+in+retina.">Pyruvate kinase and aspartate-glutamate carrier distributions reveal key metabolic links between neurons and glia in retina.</a> Proceedings of the National Academy of Sciences U. S. A. 111 (43), 15579-15584 (2014).</li><li>Cowan, C. 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=Cell+types+of+the+human+retina+and+its+organoids+at+single-cell+resolution.">Cell types of the human retina and its organoids at single-cell resolution.</a> Cell. 182 (6), 1623-1640 (2020).</li><li>Kruczek, K., Swaroop, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pluripotent+stem+cell-derived+retinal+organoids+for+disease+modeling+and+development+of+therapies.">Pluripotent stem cell-derived retinal organoids for disease modeling and development of therapies.</a> Stem Cells. 38 (10), 1206-1215 (2020).</li><li>Sinha, D., Phillips, J., Phillips, M. J., Gamm, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mimicking+retinal+development+and+disease+with+human+pluripotent+stem+cells.">Mimicking retinal development and disease with human pluripotent stem cells.</a> Investigative Ophthalmology and Visual Science. 57 (5), 1-9 (2016).</li><li>Gan, L., Cookson, M. R., Petrucelli, L., La Spada, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Converging+pathways+in+neurodegeneration,+from+genetics+to+mechanisms.">Converging pathways in neurodegeneration, from genetics to mechanisms.</a> Nature Neuroscience. 21 (10), 1300-1309 (2018).</li><li>Aung, K. Z., Wickremasinghe, S. S., Makeyeva, G., Robman, L., Guymer, R. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+prevalence+estimates+of+macular+telangiectasia+type+2:+the+Melbourne+collaborative+cohort+study.">The prevalence estimates of macular telangiectasia type 2: the Melbourne collaborative cohort study.</a> Retina. 30 (3), 473-478 (2010).</li><li>Chew, E. 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=Effect+of+ciliary+neurotrophic+factor+on+retinal+neurodegeneration+in+patients+with+macular+telangiectasia+type+2:+A+randomized+clinical+trial.">Effect of ciliary neurotrophic factor on retinal neurodegeneration in patients with macular telangiectasia type 2: A randomized clinical trial.</a> Ophthalmology. 126 (4), 540-549 (2019).</li><li>Gass, J. D., Blodi, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Idiopathic+juxtafoveolar+retinal+telangiectasis.+Update+of+classification+and+follow-up+study.">Idiopathic juxtafoveolar retinal telangiectasis. Update of classification and follow-up study.</a> Ophthalmology. 100 (10), 1536-1546 (1993).</li><li>Klein, 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+prevalence+of+macular+telangiectasia+type+2+in+the+Beaver+Dam+eye+study.">The prevalence of macular telangiectasia type 2 in the Beaver Dam eye study.</a> American Journal of Ophthalmology. 150 (1), 55-62 (2010).</li><li>Powner, M. B., 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=Loss+of+Muller's+cells+and+photoreceptors+in+macular+telangiectasia+type+2.">Loss of Muller's cells and photoreceptors in macular telangiectasia type 2.</a> Ophthalmology. 120 (11), 2344-2352 (2013).</li><li>Gantner, M. 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=Serine+and+lipid+metabolism+in+macular+disease+and+peripheral+neuropathy.">Serine and lipid metabolism in macular disease and peripheral neuropathy.</a> New England Journal of Medicine. 381 (15), 1422-1433 (2019).</li><li>Scerri, T. 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=Genome-wide+analyses+identify+common+variants+associated+with+macular+telangiectasia+type+2.">Genome-wide analyses identify common variants associated with macular telangiectasia type 2.</a> Nature Genetics. 49 (4), 559-567 (2017).</li><li>Alecu, I., 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=Cytotoxic+1-deoxysphingolipids+are+metabolized+by+a+cytochrome+P450-dependent+pathway.">Cytotoxic 1-deoxysphingolipids are metabolized by a cytochrome P450-dependent pathway.</a> Journal of Lipid Research. 58 (1), 60-71 (2017).</li><li>Othman, 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=Fenofibrate+lowers+atypical+sphingolipids+in+plasma+of+dyslipidemic+patients:+A+novel+approach+for+treating+diabetic+neuropathy.">Fenofibrate lowers atypical sphingolipids in plasma of dyslipidemic patients: A novel approach for treating diabetic neuropathy.</a> Journal of Clinical Lipidology. 9 (4), 568-575 (2015).</li><li>Ohlemacher, S. K., Iglesias, C. L., Sridhar, A., Gamm, D. M., Meyer, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generation+of+highly+enriched+populations+of+optic+vesicle-like+retinal+cells+from+human+pluripotent+stem+cells.">Generation of highly enriched populations of optic vesicle-like retinal cells from human pluripotent stem cells.</a> Curr Protoc Stem Cell Biol. 32, 1-20 (2015).</li><li>Zhong, X., 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=Generation+of+three-dimensional+retinal+tissue+with+functional+photoreceptors+from+human+iPSCs.">Generation of three-dimensional retinal tissue with functional photoreceptors from human iPSCs.</a> Nature Communication. 5, 4047 (2014).</li><li>Eiraku, 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=Self-organizing+optic-cup+morphogenesis+in+three-dimensional+culture.">Self-organizing optic-cup morphogenesis in three-dimensional culture.</a> Nature. 472 (7341), 51-56 (2011).</li><li>Wahlin, K. 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=Photoreceptor+outer+segment-like+structures+in+long-term+3D+retinas+from+human+pluripotent+stem+cells.">Photoreceptor outer segment-like structures in long-term 3D retinas from human pluripotent stem cells.</a> Science Reports. 7 (1), 766 (2017).</li><li>Capowski, E. E., 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=Reproducibility+and+staging+of+3D+human+retinal+organoids+across+multiple+pluripotent+stem+cell+lines.">Reproducibility and staging of 3D human retinal organoids across multiple pluripotent stem cell lines.</a> Development. 146 (1), (2019).</li><li>Luo, 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=An+optimized+system+for+effective+derivation+of+three-dimensional+retinal+tissue+via+Wnt+signaling+regulation.">An optimized system for effective derivation of three-dimensional retinal tissue via Wnt signaling regulation.</a> Stem Cells. 36 (11), 1709-1722 (2018).</li><li>Ovando-Roche, 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=Use+of+bioreactors+for+culturing+human+retinal+organoids+improves+photoreceptor+yields.">Use of bioreactors for culturing human retinal organoids improves photoreceptor yields.</a> Stem Cell Research Therapy. 9 (1), 156 (2018).</li></ol>

Differentiation protocol variations 
Since the invention of self-forming optic cups by Yoshiki Sasai&#39;s group20, many labs have developed protocols to generate retinal organoids that can vary at almost every step5,18,19,21. An exhaustive list of protocols can be found in Capowski et al.22. The differentiation protocol we p...

Modeling human disease in cell culture and animal models has provided invaluable tools for the discovery, modification, and validation of pharmacologic therapeutics, allowing them to advance from candidate drug to approved therapy. Although a combination of in vitro and non-human in vivo models has long been a critical component of the drug development pipeline they frequently fail to predict the clinical performance of novel drug candidates1. There is a clear need for the development of technologies that bridge the gap between simplistic human cellular monocultures and clinical trials. Recent technological advances in self-organized three-dimensional tissue cultures, organoids, have improved their fidelity to the tissues they model making them promising tools in the preclinical drug development pipeline2.
A major advantage of human cell culture over non-human in vivo models is the ability to replicate the specific intricacies of human metabolism which can vary considerably even between higher order vertebrates such as humans and mice3. However, this specificity can be overshadowed by a loss in tissue complexity; such is the case for retinal tissue where multiple cell types are intricately interwoven and have a unique symbiotic metabolic interplay between cellular subtypes that cannot be replicated in a monoculture4. Human organoids, which provide a facsimile of complex human tissues with the accessibility and scalability of cell culture, have the potential to overcome the deficiencies of these disease modeling platforms.
Retinal organoids derived from stem cells have proven to be particularly faithful in modeling the complex tissue of the human neural retina5. This has made the retinal organoid model a promising technology for the study and treatment of retinal disease6,7. To date much of the disease modeling in retinal organoids has focused on monogenic retinal diseases where retinal organoids are derived from iPSC lines with disease-causing genetic variants7. These are generally highly penetrant mutations that manifest as developmental phenotypes. Less work has been effectively done on aging diseases where genetic mutations and environmental stressors impact tissue that has developed normally. Neurodegenerative diseases of aging can have complex genetic inheritance and contributions from environmental stressors that are inherently difficult to model using short-term cell cultures. However, in many cases these complex diseases can coalesce on common cellular or metabolic stressors that, when tested on a fully developed human tissue, can provide powerful insights into neurodegenerative diseases of aging8.
The late-onset macular degenerative disease, macular telangiectasia type II (MacTel), is a great example of a genetically complex neurodegenerative disease that coalesces on a common metabolic defect. MacTel is an uncommon retinal degenerative disease of aging that results in photoreceptor and M&#252;ller glia loss in the macula, leading to a progressive loss in central vision9,10,11,12,13. In MacTel, an undetermined, possibly multifactorial, genetic inheritance drives a common reduction in circulating serine in patients, resulting in an increase in a neurotoxic lipid species called deoxysphingolipids (deoxySL)14,15. To prove that accumulation of deoxySL is toxic to the retina and to validate potential pharmaceutical therapeutics, we developed this protocol to assay photoreceptor toxicity in human retinal organoids14.
Here we outline a specific protocol for differentiating human retinal organoids, establishing a toxicity and rescue assay using organoids, and quantifying outcomes. We provide a successful example where we determine the tissue-specific toxicity of a suspected disease-causing agent, deoxySL, and validate the use of a safe generic drug, fenofibrate, for the potential treatment of deoxySL-induced retinal toxicity. Previous work has shown that fenofibrate can increase the degradation of deoxySL and lower circulating deoxySL in patients, however, its efficacy in reducing deoxySL-induced retinal toxicity has not been tested16,17. Although we present a specific example, this protocol can be utilized to evaluate the effect of any number of metabolic/environmental stressors and potential therapeutic drugs on retinal tissue.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.5M EDTA</td>
			<td>Invitrogen</td>
			<td>15575020</td>
			<td></td>
		</tr>
		<tr>
			<td>125mL Erlenmeyer Flasks</td>
			<td>VWR</td>
			<td>89095-258</td>
			<td></td>
		</tr>
		<tr>
			<td>1-deoxysphinganine</td>
			<td>Avanti</td>
			<td>860493</td>
			<td></td>
		</tr>
		<tr>
			<td>B27 Supplement, minus vitamin A</td>
			<td>Gibco</td>
			<td>12587010</td>
			<td></td>
		</tr>
		<tr>
			<td>Beaver 6900 Mini-Blade</td>
			<td>Beaver-Visitec</td>
			<td>BEAVER6900</td>
			<td></td>
		</tr>
		<tr>
			<td>D-(+)-Sucrose</td>
			<td>VWR</td>
			<td>97061-432</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>Thermo-fisher</td>
			<td>D1306</td>
			<td></td>
		</tr>
		<tr>
			<td>Dispase II, powder</td>
			<td>Gibco</td>
			<td>17105041</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM, high glucose, pyruvate</td>
			<td>Gibco</td>
			<td>11995073</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM/F12</td>
			<td>Gibco</td>
			<td>11330</td>
			<td></td>
		</tr>
		<tr>
			<td>Donkey anti-rabbit Ig-G, Alexa Fluor plus 555</td>
			<td>Thermo-fisher</td>
			<td>A32794</td>
			<td></td>
		</tr>
		<tr>
			<td>donkey serum</td>
			<td>Sigma</td>
			<td>D9663-10ML</td>
			<td></td>
		</tr>
		<tr>
			<td>FBS, Heat Inactivated</td>
			<td>Corning</td>
			<td>45001-108</td>
			<td></td>
		</tr>
		<tr>
			<td>Fenofibrate</td>
			<td>Sigma</td>
			<td>F6020</td>
			<td></td>
		</tr>
		<tr>
			<td>Glutamax</td>
			<td>Gibco</td>
			<td>35050061</td>
			<td></td>
		</tr>
		<tr>
			<td>Heparin</td>
			<td>Stemcell Technologies</td>
			<td>7980</td>
			<td></td>
		</tr>
		<tr>
			<td>In Situ Cell Death Detection Kit, Fluorescin</td>
			<td>Sigma</td>
			<td>11684795910</td>
			<td></td>
		</tr>
		<tr>
			<td>Matrigel, growth factor reduced</td>
			<td>Corning</td>
			<td>356230</td>
			<td></td>
		</tr>
		<tr>
			<td>MEM Non-Essential Amino Acids Solution</td>
			<td>Gibco</td>
			<td>11140050</td>
			<td></td>
		</tr>
		<tr>
			<td>mTeSR 1</td>
			<td>Stemcell Technologies</td>
			<td>85850</td>
			<td></td>
		</tr>
		<tr>
			<td>N2 Supplement</td>
			<td>Gibco</td>
			<td>17502048</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>Gibco</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>Pierce 16% Formaldehyde</td>
			<td>Thermo-fisher</td>
			<td>28906</td>
			<td></td>
		</tr>
		<tr>
			<td>Rabbit anti-Recoverin antibody</td>
			<td>Millipore</td>
			<td>AB5585</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Citrate</td>
			<td>Sigma</td>
			<td>W302600</td>
			<td></td>
		</tr>
		<tr>
			<td>Steriflip Sterile Disposable Vacuum Filter Units</td>
			<td>MilliporeSigma</td>
			<td>SE1M179M6</td>
			<td></td>
		</tr>
		<tr>
			<td>Taurine</td>
			<td>Sigma</td>
			<td>T0625</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue Plus- O.C.T. compound</td>
			<td>Fisher Scientific</td>
			<td>23-730-571</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue-Tek Cryomold</td>
			<td>EMS</td>
			<td>62534-10</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Sigma</td>
			<td>X100</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Sigma</td>
			<td>P1379</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultra-Low Attachment 6 well Plates</td>
			<td>Corning</td>
			<td>29443-030</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultra-Low Attachment 75cm2 U-Flask</td>
			<td>Corning</td>
			<td>3814</td>
			<td></td>
		</tr>
		<tr>
			<td>Vacuum Filtration System</td>
			<td>VWR</td>
			<td>10040-436</td>
			<td></td>
		</tr>
		<tr>
			<td>Vectashield-mounting medium</td>
			<td>vector Labs</td>
			<td>H-1000</td>
			<td></td>
		</tr>
		<tr>
			<td>wax pen-ImmEdge</td>
			<td>vector Labs</td>
			<td>H-4000</td>
			<td></td>
		</tr>
		<tr>
			<td>Y-27632 Dihydrochloride (Rock inhibitor)</td>
			<td>Sigma</td>
			<td>Y0503</td>
			<td></td>
		</tr>
	</tbody>
</table>

toxicity screens in human retinal organoids for pharmaceutical discovery

Organoids provide a promising platform to study disease mechanism and treatments, directly in the context of human tissue with the versatility and throughput of cell culture. Mature human retinal organoids are utilized to screen potential pharmaceutical treatments for the age-related retinal degenerative disease macular telangiectasia type 2 (MacTel).
We have recently shown that MacTel can be caused by elevated levels of an atypical lipid species, deoxysphingolipids (deoxySLs). These lipids are toxic to the retina and may drive the photoreceptor loss that occurs in MacTel patients. To screen drugs for their ability to prevent deoxySL photoreceptor toxicity, we generated human retinal organoids from a non-MacTel induced pluripotent stem cell (iPSC) line and matured them to a post-mitotic age where they develop all of the neuronal lineage-derived cells of the retina, including functionally mature photoreceptors. The retinal organoids were treated with a deoxySL metabolite and apoptosis was measured within the photoreceptor layer using immunohistochemistry. Using this toxicity model, pharmacological compounds that prevent deoxySL-induced photoreceptor death were screened. Using a targeted candidate approach, we determined that fenofibrate, a drug commonly prescribed for the treatment of high cholesterol and triglycerides, can also prevent deoxySL toxicity in the cells of the retina.
The toxicity screen successfully identified an FDA-approved drug that can prevent photoreceptor death. This is a directly actionable finding owing to the highly disease-relevant model tested. This platform can be easily modified to test any number of metabolic stressors and potential pharmacological interventions for future treatment discovery in retinal diseases.

Retinal organoids were generated from a non-MacTel control iPSC line. After organoids reached 26 weeks in culture they were selected and split into experimental groups. Organoids were treated with varying concentrations of deoxySA to determine if deoxySA is toxic to photoreceptors. Four concentrations of deoxySA were tested, from 0 to 1 &#181;M (Figure 2) and organoids were treated for 8 days, with media changes every other day. Cell death in response to deoxySA is concentration-dependent an...

Watch this Scientific Journal Video about Toxicity Screens in Human Retinal Organoids for Pharmaceutical Discovery at JoVE.com

Toxicity Screens in Human Retinal Organoids for Pharmaceutical Discovery

Here we present a step-by-step protocol to generate mature human retinal organoids and utilize them in a photoreceptor toxicity assay to identify pharmaceutical candidates for the age-related retinal degenerative disease macular telangiectasia type 2 (MacTel).

Organoids provide a promising platform to study disease mechanism and treatments, directly in the context of human tissue with the versatility and ...

This protocol provides a preclinical approach to discovering and validating pharmaceutical treatments for the metabolic retinal diseases directly within human retinal tissue. This technique combines the complexity of metabolism in human tissues with the versatility and throughput of cell culture. We have used this assay to acquire preclinical data for treatment of the retinal degenerative disease, MacTel, using a common and safe lipid altering drug, fenofibrate, which is now in clinical safety trials.This approach can be applied to any number of common retinal stressors that lead to disease including nutrient deficiency, hypoxia, light toxicity, and other toxic lipids. At week 24 of culture, check the organoids for the formation of rudimentary segments on the outside of the organoid. By week 26 to 28, the outer segments should have formed a thick layer.When a thickened doubter segment can be observed, dilute one millimolar deoxySA stock solution to 0.51. One and two micromolar concentrations in three milliliters of retinal differentiation medium plus. Using a dissection microscope and a sterile probe, select four groups of organoids of approximately the same size and shape with a minimum of five organoids per group, and split the groups into individual wells of an ultra-low attachment 6-well plate.When all of the organoids have been collected, remove as much medium from each well as possible and add one concentration of the deoxySA solution to each well. Add the vehicle control to the fourth group of organoids. After two days of culture, replace the culture supernatants with the appropriate fresh deoxySA or control dilution.After four days of culture, embed cryo section and stain the organoids according to standard protocols to allow assessment of the cell death within each culture. After staining, use a five to 10x magnification to locate a region of the sliced organoid section that is intact, well formed, and in a plane that samples a representative cross section of the organoid. The section should have a distinct outer nuclear layer of photoreceptors that is at least a few cells thick, and a separate and distinct layer of nuclei that do not have recover and staining.Frame the image and increase the magnification to 20x. Then, frame the slide again to fill the image with as much of the photoreceptor layer as possible. Set the Z-plane and set the upper end lower limits of the Z-range to image the entire depth of the slice.Then image all three channels of fluorophore in a Z-stack acquisition, and save the image in a file format that preserves the ratio of area per pixel. To quantify the number of dead cells in each sample, open the image stacks in Fiji. In the bio format's import options window, confirm that no boxes under the split into separate windows section are checked and select Image, Stacks, and Z project to create a new image for quantification.Select the image channel that shows the recover and staining and use the polygon selection tool to outline a continuous region of photoreceptors in the image. Click Analyze and Set Measurements and select the Area box. Click Analyze and Measure, to measure the area of the photoreceptors, to count the dying cells.The measurement will appear in a pop-up window. To count the apoptosis positive nuclei in the selected photoreceptor region, right click on the point tool to select the multipoint tool and select the apoptosis positive staining that overlaps with a DAPI positive nuclei and recover and staining. Toggle between the channels to validate the positive cells.Then divide the number of apoptosis positive cells by the area to obtain a normalized value for the cell death within the photoreceptors per organoid. After determining the deoxySA concentration that induces the target cell death, use a sterile probe to select three groups of organoids of approximately the same size and shape with a minimum of five organoids per group. And add the groups to individual wells of an ultra-low attachment 6-well plate.Add the target cell death concentration of deoxySA, the target cell death concentration of deoxySA supplemented with the drug of interest or the control medium to the appropriate well or organoids. After two days, replace the supernatant in each well with the appropriate concentration of fresh treatment or control medium. After four days of culture, assess the cultures for cell death as demonstrated.In this representative analysis, retinal organoids generated from a non macular telangiectasia type 2 control induced pluripotent stem cell line were treated with four concentrations of deoxySA. Cell death in response to deoxySA was concentration dependent and detectable in as little as 50 nanomolar deoxySA. The highest concentration tested induced a robust cell death while still maintaining the integrity of the retinal organoid.Treatment with 20 micromolar fenofibrate prevented deoxySA induced toxicity in the photo receptors of retinal organoids, significantly reducing cell death by approximately 80%after four days of treatment. Remember to select well formed and healthy organoids to ensure that the assay is being performed in retinal cells. The organoids can be processed for RNA collection to quantify gene expression, allowing the evaluation of stress signals and the validation of toxic effects and rescues.Using this technique, we have been able to assay the downstream metabolism of multiple different lipids in organoids, opening up the study of lipid metabolism in human retinas.

toxicity-screens-human-retinal-organoids-for-pharmaceutical

Research

JoVE Journal

Bioengineering

Fluorescent Nanoparticles for the Measurement of Ion Concentration in Biological Systems

Tightly regulated ion homeostasis throughout the body is necessary for the prevention of such debilitating states as dehydration.1 In contrast, rapid ion fluxes at the cellular level are required for initiating action potentials in excitable cells.2 Sodium regulation plays an important role in both of these cases; however, no method currently exists for continuously monitoring sodium levels in vivo 3 and intracellular sodium probes 4 do not provide similar detailed results as calcium probes. In an effort to fill both of these voids, fluorescent nanosensors have been developed that can monitor sodium concentrations in vitro and in vivo.5,6 These sensors are based on ion-selective optode technology and consist of plasticized polymeric particles in which sodium specific recognition elements, pH-sensitive fluorophores, and additives are embedded.7-9 Mechanistically, the sodium recognition element extracts sodium into the sensor. 10 This extraction causes the pH-sensitive fluorophore to release a hydrogen ion to maintain charge neutrality within the sensor which causes a change in fluorescence. The sodium sensors are reversible and selective for sodium over potassium even at high intracellular concentrations.6 They are approximately 120 nm in diameter and are coated with polyethylene glycol to impart biocompatibility. Using microinjection techniques, the sensors can be delivered into the cytoplasm of cells where they have been shown to monitor the temporal and spatial sodium dynamics of beating cardiac myocytes.11 Additionally, they have also tracked real-time changes in sodium concentrations in vivo when injected subcutaneously into mice.3 Herein, we explain in detail and demonstrate the methodology for fabricating fluorescent sodium nanosensors and briefly demonstrate the biological applications our lab uses the nanosensors for: the microinjection of the sensors into cells; and the subcutaneous injection of the sensors into mice.

Fluorescent nanoparticles produced in our lab are used for imaging ion concentrations and ion fluxes in biological systems such as cells during signaling and interstitial fluid during physiological homeostasis.

Tightly regulated ion homeostasis throughout the body is necessary for the prevention of such debilitating states as dehydration.1 In contrast, rapid ion ...

GENPLAT: an Automated Platform for Biomass Enzyme Discovery and Cocktail Optimization

The high cost of enzymes for biomass deconstruction is a major impediment to the economic conversion of lignocellulosic feedstocks to liquid transportation fuels such as ethanol. We have developed an integrated high throughput platform, called GENPLAT, for the discovery and development of novel enzymes and enzyme cocktails for the release of sugars from diverse pretreatment/biomass combinations. GENPLAT comprises four elements: individual pure enzymes, statistical design of experiments, robotic pipeting of biomass slurries and enzymes, and automated colorimeteric determination of released Glc and Xyl. Individual enzymes are produced by expression in Pichia pastoris or Trichoderma reesei, or by chromatographic purification from commercial cocktails or from extracts of novel microorganisms. Simplex lattice (fractional factorial) mixture models are designed using commercial Design of Experiment statistical software. Enzyme mixtures of high complexity are constructed using robotic pipeting into a 96-well format. The measurement of released Glc and Xyl is automated using enzyme-linked colorimetric assays. Optimized enzyme mixtures containing as many as 16 components have been tested on a variety of feedstock and pretreatment combinations.
GENPLAT is adaptable to mixtures of pure enzymes, mixtures of commercial products (e.g., Accellerase 1000 and Novozyme 188), extracts of novel microbes, or combinations thereof. To make and test mixtures of &tilde;10 pure enzymes requires less than 100 &mu;g of each protein and fewer than 100 total reactions, when operated at a final total loading of 15 mg protein/g glucan. We use enzymes from several sources. Enzymes can be purified from natural sources such as fungal cultures (e.g., Aspergillus niger, Cochliobolus carbonum, and Galerina marginata), or they can be made by expression of the encoding genes (obtained from the increasing number of microbial genome sequences) in hosts such as E. coli, Pichia pastoris, or a filamentous fungus such as T. reesei. Proteins can also be purified from commercial enzyme cocktails (e.g., Multifect Xylanase, Novozyme 188). An increasing number of pure enzymes, including glycosyl hydrolases, cell wall-active esterases, proteases, and lyases, are available from commercial sources, e.g., Megazyme, Inc. (www.megazyme.com), NZYTech (www.nzytech.com), and PROZOMIX (www.prozomix.com).
Design-Expert software (Stat-Ease, Inc.) is used to create simplex-lattice designs and to analyze responses (in this case, Glc and Xyl release). Mixtures contain 4-20 components, which can vary in proportion between 0 and 100%. Assay points typically include the extreme vertices with a sufficient number of intervening points to generate a valid model. In the terminology of experimental design, most of our studies are "mixture" experiments, meaning that the sum of all components adds to a total fixed protein loading (expressed as mg/g glucan). The number of mixtures in the simplex-lattice depends on both the number of components in the mixture and the degree of polynomial (quadratic or cubic). For example, a 6-component experiment will entail 63 separate reactions with an augmented special cubic model, which can detect three-way interactions, whereas only 23 individual reactions are necessary with an augmented quadratic model. For mixtures containing more than eight components, a quadratic experimental design is more practical, and in our experience such models are usually statistically valid.
All enzyme loadings are expressed as a percentage of the final total loading (which for our experiments is typically 15 mg protein/g glucan). For "core" enzymes, the lower percentage limit is set to 5%. This limit was derived from our experience in which yields of Glc and/or Xyl were very low if any core enzyme was present at 0%. Poor models result from too many samples showing very low Glc or Xyl yields. Setting a lower limit in turn determines an upper limit. That is, for a six-component experiment, if the lower limit for each single component is set to 5%, then the upper limit of each single component will be 75%. The lower limits of all other enzymes considered as "accessory" are set to 0%. "Core" and "accessory" are somewhat arbitrary designations and will differ depending on the substrate, but in our studies the core enzymes for release of Glc from corn stover comprise the following enzymes from T. reesei: CBH1 (also known as Cel7A), CBH2 (Cel6A), EG1(Cel7B), BG (&beta;-glucosidase), EX3 (endo-&beta;1,4-xylanase, GH10), and BX (&beta;-xylosidase).
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GENPLAT (GLBRC Enzyme Platform) is an automated platform for discovery and optimization of enzyme cocktails for biomass degradation. It can be adapted to multiple feedstocks and mixtures of enzymes containing multiple components.

The high cost of enzymes for biomass deconstruction is a major impediment to the economic conversion of lignocellulosic feedstocks to liquid ...

Therapeutic Gene Delivery and Transfection in Human Pancreatic Cancer Cells using Epidermal Growth Factor Receptor-targeted Gelatin Nanoparticles

More than 32,000 patients are diagnosed with pancreatic cancer in the United States per year and the disease is associated with very high mortality 1. Urgent need exists to develop novel clinically-translatable therapeutic strategies that can improve on the dismal survival statistics of pancreatic cancer patients. Although gene therapy in cancer has shown a tremendous promise, the major challenge is in the development of safe and effective delivery system, which can lead to sustained transgene expression. 
Gelatin is one of the most versatile natural biopolymer, widely used in food and pharmaceutical products. Previous studies from our laboratory have shown that type B gelatin could physical encapsulate DNA, which preserved the supercoiled structure of the plasmid and improved transfection efficiency upon intracellular delivery. By thiolation of gelatin, the sulfhydryl groups could be introduced into the polymer and would form disulfide bond within nanoparticles, which stabilizes the whole complex and once disulfide bond is broken due to the presence of glutathione in cytosol, payload would be released 2-5. Poly(ethylene glycol) (PEG)-modified GENS, when administered into the systemic circulation, provides long-circulation times and preferentially targets to the tumor mass due to the hyper-permeability of the neovasculature by the enhanced permeability and retention effect 6. Studies have shown over-expression of the epidermal growth factor receptor (EGFR) on Panc-1 human pancreatic adenocarcinoma cells 7. In order to actively target pancreatic cancer cell line, EGFR specific peptide was conjugated on the particle surface through a PEG spacer.8
Most anti-tumor gene therapies are focused on administration of the tumor suppressor genes, such as wild-type p53 (wt-p53), to restore the pro-apoptotic function in the cells 9. The p53 mechanism functions as a critical signaling pathway in cell growth, which regulates apoptosis, cell cycle arrest, metabolism and other processes 10. In pancreatic cancer, most cells have mutations in p53 protein, causing the loss of apoptotic activity. With the introduction of wt-p53, the apoptosis could be repaired and further triggers cell death in cancer cells 11. 
Based on the above rationale, we have designed EGFR targeting peptide-modified thiolated gelatin nanoparticles for wt-p53 gene delivery and evaluated delivery efficiency and transfection in Panc-1 cells.

Type B gelatin-based engineered nanovectors system (GENS) was developed for systemic gene delivery and transfection in the treatment of pancreatic cancer. By modification with epidermal growth factor receptor (EGFR) specific peptide on the surface of nanparticles, they could target on EGFR receptor and release plasmid under reducing environment, such as high intracellular glutathione concentrations.

More than 32,000 patients are diagnosed with pancreatic cancer in the United States per year and the disease is associated with very high mortality 1. ...

Polymer Microarrays for High Throughput Discovery of Biomaterials

The discovery of novel biomaterials that are optimized for a specific biological application is readily achieved using polymer microarrays, which allows a combinatorial library of materials to be screened in a parallel, high throughput format1. Herein is described the formation and characterization of a polymer microarray using an on-chip photopolymerization technique 2. This involves mixing monomers at varied ratios to produce a library of monomer solutions, transferring the solution to a glass slide format using a robotic printing device and curing with UV irradiation. This format is readily amenable to many biological assays, including stem cell attachment and proliferation, cell sorting and low bacterial adhesion, allowing the ready identification of 'hit' materials that fulfill a specific biological criterion3-5. Furthermore, the use of high throughput surface characterization (HTSC) allows the biological performance to be correlated with physio-chemical properties, hence elucidating the biological-material interaction6. HTSC makes use of water contact angle (WCA) measurements, atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). In particular, ToF-SIMS provides a chemically rich analysis of the sample that can be used to correlate the cell response with a molecular moiety. In some cases, the biological performance can be predicted from the ToF-SIMS spectra, demonstrating the chemical dependence of a biological-material interaction, and informing the development of hit materials5,3.

A description of the formation of a polymer microarray using an on-chip photopolymerization technique. The high throughput surface characterization using atomic force microscopy, water contact angle measurements, X-ray photoelectron spectroscopy and time of flight secondary ion mass spectrometry and a cell attachment assay is also described.

The discovery of novel biomaterials that are optimized for a specific biological application is readily achieved using polymer microarrays, which allows a ...

Low Molecular Weight Protein Enrichment on Mesoporous Silica Thin Films for Biomarker Discovery

The identification of circulating biomarkers holds great potential for non invasive approaches in early diagnosis and prognosis, as well as for the monitoring of therapeutic efficiency.1-3 The circulating low molecular weight proteome (LMWP) composed of small proteins shed from tissues and cells or peptide fragments derived from the proteolytic degradation of larger proteins, has been associated with the pathological condition in patients and likely reflects the state of disease.4,5 Despite these potential clinical applications, the use of Mass Spectrometry (MS) to profile the LMWP from biological fluids has proven to be very challenging due to the large dynamic range of protein and peptide concentrations in serum.6 Without sample pre-treatment, some of the more highly abundant proteins obscure the detection of low-abundance species in serum/plasma. Current proteomic-based approaches, such as two-dimensional polyacrylamide gel-electrophoresis (2D-PAGE) and shotgun proteomics methods are labor-intensive, low throughput and offer limited suitability for clinical applications.7-9 Therefore, a more effective strategy is needed to isolate LMWP from blood and allow the high throughput screening of clinical samples. 
Here, we present a fast, efficient and reliable multi-fractionation system based on mesoporous silica chips to specifically target and enrich LMWP.10,11 Mesoporous silica (MPS) thin films with tunable features at the nanoscale were fabricated using the triblock copolymer template pathway. Using different polymer templates and polymer concentrations in the precursor solution, various pore size distributions, pore structures, connectivity and surface properties were determined and applied for selective recovery of low mass proteins. The selective parsing of the enriched peptides into different subclasses according to their physicochemical properties will enhance the efficiency of recovery and detection of low abundance species. In combination with mass spectrometry and statistic analysis, we demonstrated the correlation between the nanophase characteristics of the mesoporous silica thin films and the specificity and efficacy of low mass proteome harvesting. The results presented herein reveal the potential of the nanotechnology-based technology to provide a powerful alternative to conventional methods for LMWP harvesting from complex biological fluids. Because of the ability to tune the material properties, the capability for low-cost production, the simplicity and rapidity of sample collection, and the greatly reduced sample requirements for analysis, this novel nanotechnology will substantially impact the field of proteomic biomarker research and clinical proteomic assessment.

We developed a technology based on mesoporous silica thin film for the selective recovery of low molecular weight proteins and peptides from human serum. The physico-chemical properties of our mesoporous chips were finely tuned to provide substantial control in peptide enrichment and consequently profile the serum proteome for diagnostic purposes.

The identification of circulating biomarkers holds great potential for non invasive approaches in early diagnosis and prognosis, as well as for the ...

Isolation of Primary Murine Retinal Ganglion Cells (RGCs) by Flow Cytometry

Neurodegenerative diseases often have a devastating impact on those affected. Retinal ganglion cell (RGC) loss is implicated in an array of diseases, including diabetic retinopathy and glaucoma, in addition to normal aging. Despite their importance, RGCs have been extremely difficult to study until now due in part to the fact that they comprise only a small percentage of the wide variety of cells in the retina. In addition, current isolation methods use intracellular markers to identify RGCs, which produce non-viable cells. These techniques also involve lengthy isolation protocols, so there is a lack of practical, standardized, and dependable methods to obtain and isolate RGCs. This work describes an efficient, comprehensive, and reliable method to isolate primary RGCs from mice retinae using a protocol based on both positive and negative selection criteria. The presented methods allow for the future study of RGCs, with the goal of better understanding the major decline in visual acuity that results from the loss of functional RGCs in neurodegenerative diseases.

Isolation of Primary Murine Retinal Ganglion Cells RGCs by Flow Cytometry

Millions of people suffer from retinal degenerative diseases that result in irreversible blindness. A common element of many of these diseases is the loss of retinal ganglion cells (RGCs). This detailed protocol describes the isolation of primary murine RGCs by positive and negative selection with flow cytometry.

Neurodegenerative diseases often have a devastating impact on those affected. Retinal ganglion cell (RGC) loss is implicated in an array of diseases, ...

Microfluidic Bioprinting for Engineering Vascularized Tissues and Organoids

Engineering vascularized tissue constructs and organoids has been historically challenging. Here we describe a novel method based on microfluidic bioprinting to generate a scaffold with multilayer interlacing hydrogel microfibers. To achieve smooth bioprinting, a core-sheath microfluidic printhead containing a composite bioink formulation extruded from the core flow and the crosslinking solution carried by the sheath flow, was designed and fitted onto the bioprinter. By blending gelatin methacryloyl (GelMA) with alginate, a polysaccharide that undergoes instantaneous ionic crosslinking in the presence of select divalent ions, followed by a secondary photocrosslinking of the GelMA component to achieve permanent stabilization, a microfibrous scaffold could be obtained using this bioprinting strategy. Importantly, the endothelial cells encapsulated inside the bioprinted microfibers can form the lumen-like structures resembling the vasculature over the course of culture for 16 days. The endothelialized microfibrous scaffold may be further used as a vascular bed to construct a vascularized tissue through subsequent seeding of the secondary cell type into the interstitial space of the microfibers. Microfluidic bioprinting provides a generalized strategy in convenient engineering of vascularized tissues at high fidelity.

We provide a generalized protocol based on a microfluidic bioprinting strategy for engineering a microfibrous vascular bed, where a secondary cell type could be further seeded into the interstitial space of this microfibrous structure to generate vascularized tissues and organoids.

Engineering vascularized tissue constructs and organoids has been historically challenging. Here we describe a novel method based on microfluidic ...

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Regulation of chromatin compaction is an important process that governs gene expression in higher eukaryotes. Although chromatin compaction and gene expression regulation are commonly disrupted in many diseases, a locus-specific, endogenous, and reversible method to study and control these mechanisms of action has been lacking. To address this issue, we have developed and characterized novel gene-regulating bifunctional molecules. One component of the bifunctional molecule binds to a DNA-protein anchor so that it will be recruited to an allele-specific locus. The other component engages endogenous cellular chromatin-modifying machinery, recruiting these proteins to a gene of interest. These small molecules, called chemical epigenetic modifiers (CEMs), are capable of controlling gene expression and the chromatin environment in a dose-dependent and reversible manner. Here, we detail a CEM approach and its application to decrease gene expression and histone tail acetylation at a Green Fluorescent Protein (GFP) reporter located at the Oct4 locus in mouse embryonic stem cells (mESCs). We characterize the lead CEM (CEM23) using fluorescent microscopy, flow cytometry, and chromatin immunoprecipitation (ChIP), followed by a quantitative polymerase chain reaction (qPCR). While the power of this system is demonstrated at the Oct4 locus, conceptually, the CEM technology is modular and can be applied in other cell types and at other genomic loci.

Regulation of the chromatin environment is an essential process required for proper gene expression. Here, we describe a method for controlling gene expression through the recruitment of chromatin-modifying machinery in a gene-specific and reversible manner.

Regulation of chromatin compaction is an important process that governs gene expression in higher eukaryotes. Although chromatin compaction and gene ...

Lucifer Yellow - A Robust Paracellular Permeability Marker in a Cell Model of the Human Blood-brain Barrier

The blood-brain barrier BBB consists of endothelial cells that form a barrier between the systemic circulation and the brain to prevent the exchange of non-essential ions and toxic substances. Tight junctions (TJ) effectively seal the paracellular space in the monolayers resulting in an intact barrier. This study describes a LY-based fluorescence assay that can be used to determine its apparent permeability coefficient (Papp) and in turn can be used to determine the kinetics of the formation of confluent monolayers and the resulting tight junction barrier integrity in hCMEC/D3 monolayers. We further demonstrate an additional utility of this assay to determine TJ functional integrity in transfected cells. Our data from the LY Papp assay shows that the hCMEC/D3 cells seeded in a transwell setup effectively limit LY paracellular transport 7 days-post culture. As an additional utility of the presented assay, we also demonstrate that the DNA nanoparticle transfection does not alter LY paracellular transport in hCMEC/D3 monolayers.

We present a fluorescence assay to demonstrate that Lucifer Yellow (LY) is a robust marker to determine the apparent paracellular permeability of hCMEC/D3 cell monolayers, an in vitro model of the human blood-brain barrier. We used this assay to determine the kinetics of a confluent monolayer formation in cultured hCMEC/D3 cells.

The blood-brain barrier BBB consists of endothelial cells that form a barrier between the systemic circulation and the brain to prevent the exchange of ...

Human Neural Organoids for Studying Brain Cancer and Neurodegenerative Diseases

The lack of relevant in vitro neural models is an important obstacle on medical progress for neuropathologies. Establishment of relevant cellular models is crucial both to better understand the pathological mechanisms of these diseases and identify new therapeutic targets and strategies. To be pertinent, an in vitro model must reproduce the pathological features of a human disease. However, in the context of neurodegenerative disease, a relevant in vitro model should provide neural cell replacement as a valuable therapeutic opportunity. 
Such a model would not only allow screening of therapeutic molecules but also can be used to optimize neural protocol differentiation [for example, in the context of transplantation in Parkinson's disease (PD)]. This study describes two in vitro protocols of 1) human glioblastoma development within a human neural organoids (NO) and 2) neuron dopaminergic (DA) differentiation generating a three-dimensional (3D) organoid. For this purpose, a well-standardized protocol was established that allows the production of size-calibrated neurospheres derived from human embryonic stem cell (hESC) differentiation. The first model can be used to reveal molecular and cellular events occurring during in glioblastoma development within the neural organoid, while the DA organoid not only represents a suitable source of DA neurons for cell therapy in Parkinson's disease but also can be used for drug testing.

This study introduces and describes protocols to derive two specific human neural organoids&#160;as a relevant and accurate model for studying 1) human glioblastoma development within human neural organoids exclusively in humans and 2) neuron dopaminergic differentiation generating a three-dimensional organoid.

The lack of relevant in vitro neural models is an important obstacle on medical progress for neuropathologies. Establishment of relevant cellular models ...