Name: generating self-assembling human heart organoids derived from pluripotent stem cells
Uploaded: 2021-09-15T15:00:00
Description: Watch this Scientific Journal Video about Generating Self-Assembling Human Heart Organoids Derived from Pluripotent Stem Cells at JoVE.com

This work was supported by the National Heart, Lung, and Blood Institute of the National Institutes of Health under award numbers K01HL135464 and R01HL151505 and by the American Heart Association under award number 19IPLOI34660342. We wish to thank the MSU Advanced Microscopy Core and Dr. William Jackson at the MSU Department of Pharmacology and Toxicology for access to confocal microscopes, the IQ Microscopy Core, and the MSU Genomics Core for sequencing services. We also wish to thank all members of the Aguirre Lab for their valuable comments and advice.

1. hPSC culture and maintenance
NOTE: The human induced PSCs (hiPSCs) or human embryonic stem cells (hESCs) need to be cultured for at least 2 consecutive passages after thawing before being used to generate EBs for differentiation or further cryopreservation. hPSCs are cultured in PSC medium (see the Table of Materials) on basement-membrane-extracellular matrix (BM-ECM)-coated 6-well culture plates. When performing medium changes on hPSCs in 6-well plates, add the medium direct...

<ol>
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Recent advances in human stem cell-derived cardiomyocytes and other cells of cardiac origin have been used to model human heart development22,24,25 and disease26,27,28 and as tools to screen therapeutics29,30 and toxic agents31,<sup class="xref...

Congenital heart defects (CHDs) are the most common type of congenital defect in humans and affect approximately 1% of all live births1,2,3. Under most circumstances, the reasons for CHDs remain unknown. The ability to create human heart models in the lab that closely resemble the developing human heart constitutes a significant step forward to directly study the underlying causes of CHDs in humans rather than in surrogate animal models.
The epitome of laboratory-grown tissue models are organoids, 3D cell constructs that resemble an organ of interest in cell composition and physiological function. Organoids are often derived from stem cells or progenitor cells and have been successfully used to model many organs such as the brain4,5, kidney6,7, intestine8,9, lung10,11, liver12,13, and pancreas14,15, just to name a few. Recent studies have emerged demonstrating the feasibility of creating self-assembling heart organoids to study heart development in vitro. These models include using mouse embryonic stem cells (mESCs) to model early heart development16,17 up to atrioventricular specification18 and human pluripotent stem cells (hPSCs) to generate multi-germ layer cardiac-endoderm organoids19 and chambered cardioids20 with highly complex cellular composition.
This paper presents a novel 3-step WNT modulation protocol to generate highly complex hHOs in an efficient and cost-effective manner. Organoids are generated in 96-well plates, resulting in a scalable, high-throughput system that can be easily automated. This method relies on creating hPSC aggregates and triggering developmental steps of cardiogenesis, including mesoderm and cardiac mesoderm formation, first and second heart field specification, proepicardial organ formation, and atrioventricular specification. After 15 days of differentiation, hHOs contain all major cell lineages found in the heart, well-defined internal chambers, atrial and ventricular chambers, and a vascular network throughout the organoid. This highly sophisticated and reproducible heart organoid system is amenable to investigating structural, functional, molecular, and transcriptomic analyses in the study of heart development, and diseases, and pharmacological screening.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Antibodies</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Alexa Fluor 488 Donkey anti- mouse</td>
			<td>Invitrogen</td>
			<td>A-21202</td>
			<td>1:200</td>
		</tr>
		<tr>
			<td>Alexa Fluor 488 Donkey anti- rabbit</td>
			<td>Invitrogen</td>
			<td>A-21206</td>
			<td>1:200</td>
		</tr>
		<tr>
			<td>Alexa Fluor 594 Donkey anti- mouse</td>
			<td>Invitrogen</td>
			<td>A-21203</td>
			<td>1:200</td>
		</tr>
		<tr>
			<td>Alexa Fluor 594 Donkey anti- rabbit</td>
			<td>Invitrogen</td>
			<td>A-21207</td>
			<td>1:200</td>
		</tr>
		<tr>
			<td>Alexa Fluor 647 Donkey anti- goat</td>
			<td>Invitrogen</td>
			<td>A32849</td>
			<td>1:200</td>
		</tr>
		<tr>
			<td>HAND1</td>
			<td>Abcam</td>
			<td>ab196622</td>
			<td>Rabbit; 1:200</td>
		</tr>
		<tr>
			<td>HAND2</td>
			<td>Abcam</td>
			<td>ab200040</td>
			<td>Rabbit; 1:200</td>
		</tr>
		<tr>
			<td>NFAT2</td>
			<td>Abcam</td>
			<td>ab25916</td>
			<td>Rabbit; 1:100</td>
		</tr>
		<tr>
			<td>PECAM1</td>
			<td>DSHB</td>
			<td>P2B1</td>
			<td>Rabbit; 1:50</td>
		</tr>
		<tr>
			<td>TNNT2</td>
			<td>Abcam</td>
			<td>ab8295</td>
			<td>Mouse; 1:200</td>
		</tr>
		<tr>
			<td>THY1</td>
			<td>Abcam</td>
			<td>ab133350</td>
			<td>Rabbit; 1:200</td>
		</tr>
		<tr>
			<td>TJP1</td>
			<td>Invitrogen</td>
			<td>PA5-19090</td>
			<td>Goat; 1:250</td>
		</tr>
		<tr>
			<td>VIM</td>
			<td>Abcam</td>
			<td>ab11256</td>
			<td>Goat; 1:250</td>
		</tr>
		<tr>
			<td>WT1</td>
			<td>Abcam</td>
			<td>ab89901</td>
			<td>Rabbit; 1:200</td>
		</tr>
		<tr>
			<td>Media and Reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Accutase</td>
			<td>Innovative Cell Technologies</td>
			<td>NC9464543</td>
			<td>cell dissociation reagent</td>
		</tr>
		<tr>
			<td>Activin A</td>
			<td>R&#38;D Systems</td>
			<td>338AC010</td>
			<td></td>
		</tr>
		<tr>
			<td>B-27 Supplement (Minus Insulin)</td>
			<td>Gibco</td>
			<td>A1895601</td>
			<td>insulin-free cell culture supplement</td>
		</tr>
		<tr>
			<td>B-27 Supplement</td>
			<td>Gibco</td>
			<td>17504-044</td>
			<td>cell culture supplement</td>
		</tr>
		<tr>
			<td>BMP-4</td>
			<td>Gibco</td>
			<td>PHC9534</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin</td>
			<td>Bioworld</td>
			<td>50253966</td>
			<td></td>
		</tr>
		<tr>
			<td>CHIR-99021</td>
			<td>Selleck</td>
			<td>442310</td>
			<td></td>
		</tr>
		<tr>
			<td>D-(-)-Fructose</td>
			<td>Millipore Sigma</td>
			<td>F0127</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>Thermo Scientific</td>
			<td>62248</td>
			<td>1:1000</td>
		</tr>
		<tr>
			<td>Dimethyl Sulfoxide</td>
			<td>Millipore Sigma</td>
			<td>D2650</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM/F12</td>
			<td>Gibco</td>
			<td>10566016</td>
			<td></td>
		</tr>
		<tr>
			<td>Essential 8 Flex Medium Kit</td>
			<td>Gibco</td>
			<td>A2858501</td>
			<td>pluripotent stem cell (PSC) medium containing 1% penicillin-streptomycin</td>
		</tr>
		<tr>
			<td>Fluo4-AM</td>
			<td>Invitrogen</td>
			<td>F14201</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Millipore Sigma</td>
			<td>G5516</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Millipore Sigma</td>
			<td>410225</td>
			<td></td>
		</tr>
		<tr>
			<td>Matrigel GFR</td>
			<td>Corning</td>
			<td>CB40230</td>
			<td>Basement membrane extracellular matrix (BM-ECM)</td>
		</tr>
		<tr>
			<td>Normal Donkey Serum</td>
			<td>Millipore Sigma</td>
			<td>S30-100mL</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>MP Biomedicals</td>
			<td>IC15014601</td>
			<td>Powder dissolved in PBS Buffer &#8211; use at 4%</td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>Gibco</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffer Solution</td>
			<td>Gibco</td>
			<td>10010049</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffer Solution (10x)</td>
			<td>Gibco</td>
			<td>70011044</td>
			<td></td>
		</tr>
		<tr>
			<td>Polybead Microspheres</td>
			<td>Polysciences, Inc.</td>
			<td>73155</td>
			<td>90 &#181;m</td>
		</tr>
		<tr>
			<td>ReLeSR</td>
			<td>Stem Cell Technologies</td>
			<td>NC0729236</td>
			<td>dissociation reagent for hPSCs</td>
		</tr>
		<tr>
			<td>RPMI 1640</td>
			<td>Gibco</td>
			<td>11875093</td>
			<td></td>
		</tr>
		<tr>
			<td>Thiazovivin</td>
			<td>Millipore Sigma</td>
			<td>SML1045</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Millipore Sigma</td>
			<td>T8787</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypan Blue Solution</td>
			<td>Gibco</td>
			<td>1525006</td>
			<td></td>
		</tr>
		<tr>
			<td>VECTASHIELD Vibrance Antifade Mounting Medium</td>
			<td>Vector Laboratories</td>
			<td>H170010</td>
			<td></td>
		</tr>
		<tr>
			<td>WNT-C59</td>
			<td>Selleck</td>
			<td>NC0710557</td>
			<td></td>
		</tr>
		<tr>
			<td>Other</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>1.5 mL Microcentrifuge Tubes</td>
			<td>Fisher Scientific</td>
			<td>02682002</td>
			<td></td>
		</tr>
		<tr>
			<td>15 mL Falcon Tubes</td>
			<td>Fisher Scientific</td>
			<td>1495970C</td>
			<td></td>
		</tr>
		<tr>
			<td>2 mL Cryogenic Vials</td>
			<td>Corning</td>
			<td>13-700-500</td>
			<td></td>
		</tr>
		<tr>
			<td>50 mL Reagent Reservoirs</td>
			<td>Fisherbrand</td>
			<td>13681502</td>
			<td></td>
		</tr>
		<tr>
			<td>6-Well Flat Bottom Cell Culture Plates</td>
			<td>Corning</td>
			<td>0720083</td>
			<td></td>
		</tr>
		<tr>
			<td>8 Well chambered cover Glass with #1.5 high performance cover glass</td>
			<td>Cellvis</td>
			<td>C8-1.5H-N</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well Clear Ultra Low Attachment Microplates</td>
			<td>Costar</td>
			<td>07201680</td>
			<td></td>
		</tr>
		<tr>
			<td>ImageJ</td>
			<td>NIH</td>
			<td></td>
			<td>Image processing software</td>
		</tr>
		<tr>
			<td>Kimwipes</td>
			<td>Kimberly-Clark Professional</td>
			<td>06-666</td>
			<td>laboratory wipes</td>
		</tr>
		<tr>
			<td>Micro Cover Glass</td>
			<td>VWR</td>
			<td>48393-241</td>
			<td>24 x 50 mm No. 1.5</td>
		</tr>
		<tr>
			<td>Microscope Slides</td>
			<td>Fisherbrand</td>
			<td>1255015</td>
			<td></td>
		</tr>
		<tr>
			<td>Moxi Cell Counter</td>
			<td>Orflo Technologies</td>
			<td>&#160;MXZ001</td>
			<td></td>
		</tr>
		<tr>
			<td>Moxi Z Cell Count Cassette &#8211; Type M</td>
			<td>Orflo&#160;Technologies</td>
			<td>MXC001</td>
			<td></td>
		</tr>
		<tr>
			<td>Multichannel Pipettes</td>
			<td>Fisherbrand</td>
			<td>FBE1200300</td>
			<td>30-300 &#181;L</td>
		</tr>
		<tr>
			<td>Olympus cellVivo</td>
			<td>Olympus</td>
			<td></td>
			<td>For Caclium Imaging, analysis with Imagej</td>
		</tr>
		<tr>
			<td>Sorvall Legend X1 Centrifuge</td>
			<td>ThermoFisher Scientific</td>
			<td>75004261</td>
			<td></td>
		</tr>
		<tr>
			<td>Thermoshaker</td>
			<td>ThermoFisher Scientific</td>
			<td>13-687-711PM</td>
			<td></td>
		</tr>
		<tr>
			<td>Top Coat Nail Varish</td>
			<td>Seche Vite</td>
			<td></td>
			<td>Can purchase from any supermarket</td>
		</tr>
	</tbody>
</table>

generating self-assembling human heart organoids derived from pluripotent stem cells

The ability to study human cardiac development in health and disease is highly limited by the capacity to model the complexity of the human heart in vitro. Developing more efficient organ-like platforms that can model complex in vivo phenotypes, such as organoids and organs-on-a-chip, will enhance the ability to study human heart development and disease. This paper describes a protocol to generate highly complex human heart organoids (hHOs) by self-organization using human pluripotent stem cells and stepwise developmental pathway activation using small molecule inhibitors. Embryoid bodies (EBs) are generated in a 96-well plate with round-bottom, ultra-low attachment wells, facilitating suspension culture of individualized constructs.
The EBs undergo differentiation into hHOs by a three-step Wnt signaling modulation strategy, which involves an initial Wnt pathway activation to induce cardiac mesoderm fate, a second step of Wnt inhibition to create definitive cardiac lineages, and a third Wnt activation step to induce proepicardial organ tissues. These steps, carried out in a 96-well format, are highly efficient, reproducible, and produce large amounts of organoids per run. Analysis by immunofluorescence imaging from day 3 to day 11 of differentiation reveals first and second heart field specifications and highly complex tissues inside hHOs at day 15, including myocardial tissue with regions of atrial and ventricular cardiomyocytes, as well as internal chambers lined with endocardial tissue. The organoids also exhibit an intricate vascular network throughout the structure and an external lining of epicardial tissue. From a functional standpoint, hHOs beat robustly and present normal calcium activity as determined by Fluo-4 live imaging. Overall, this protocol constitutes a solid platform for in vitro studies in human organ-like cardiac tissues.

To achieve self-organizing hHO in vitro, we modified and combined differentiation protocols previously described for 2D monolayer differentiation of cardiomyocytes21 and epicardial cells22 using Wnt pathway modulators and for 3D precardiac organoids16 using the growth factors BMP4 and Activin A. Using the 96-well plate EB and hHO differentiation protocol described here and shown in Figure 1, the concentrations a...

Watch this Scientific Journal Video about Generating Self-Assembling Human Heart Organoids Derived from Pluripotent Stem Cells at JoVE.com

Generating Self-Assembling Human Heart Organoids Derived from Pluripotent Stem Cells

Here, we describe a protocol to create developmentally relevant human heart organoids (hHOs) efficiently using human pluripotent stem cells by self-organization. The protocol relies on the sequential activation of developmental cues and produces highly complex, functionally relevant human heart tissues.

The ability to study human cardiac development in health and disease is highly limited by the capacity to model the complexity of the human heart in ...

This protocol allows us to create a complex 3D structure that closely resembles the developing human heart in a simple cost effective way, that is reproducible across cell lines. It consists of a single protocol with three steps of differentiation, which gives rise to all the cell types of the heart, including chambers and a vascular network. This technique allows us to model a wide range of human cardiovascular diseases and to screen effective pharmacological treatments.Thanks to the high throughput nature of its design. This method is useful for investigating the developing human heart as well as diseases commonly associated with it. One of them being congenital heart defects.This protocol requires basic cell culture skills. We recommend attentive and delicate pipetting as well as gentle handling of the organoids. Begin by creating embryoid bodies or EBs two days before differentiation.Wash sub-confluent HPSCs with DBPS for at least 10 seconds. Then aspirate the DPBS. Add one milliliter of room temperature ACUTA and gently tap the plate approximately five times every minute for three to five minutes to induce detachment, while checking under the microscope.Then add one milliliter of PSC medium and Thias Avin or Thias to stop the reaction. Pipette the media up and down in the well, two to three times to generate a single cell suspension and collect the cells. Then transfer the single cell suspension to a centrifuge tube and spin for five minutes at 300 times G.Aspirate the supernatant and re-spend the cells in one milliliter of PSC medium and Thias.Dilute the cells in DPBS. Count the cells using a cell counter or hemo cystometer and dilute the cells in PSC medium with Thias to a concentration of 100, 000 cells per milliliter. Add 100 microliters of diluted cells suspension to each well of a round bottom ultra low attachment 96 well plate.Centrifuge the plate at 100 times G for three minutes and incubate for 24 hours at 37 degrees Celsius and 5%carbon dioxide. After 24 hours carefully remove 50 microliters of medium from each well and add 200 core litters of fresh PSC medium, warm to 37 degrees Celsius for a volume of 250 microliters per well. Incubate the cells for 24 hours at 37 degrees Celsius and 5%carbon dioxide.Remove 166 microliters or two thirds of medium from one side of each well, and add 166 microliters of RPMI 1640 containing insulin free B27 supplement, six micromolar cheer 990211, 0.875 nanograms per milliliter of bone morphogenetic protein four and 1.5 nanograms per milliliter of Activin A.Incubate for 24 hours at 37 degrees Celsius and 5%carbon dioxide. After 24 hours remove 166 microliters of medium from one side of each well and add 166 microliters of fresh RPMI 1640 with insulin free B27 supplement. Incubate for 24 hours at 37 degrees Celsius and 5%carbon dioxide.To induce cardiac mesoderm specification on day two, remove 166 microliters of medium from each well and add 166 microliters of RPMI 1640, containing insulin free B27 supplement and three micromolar Wnt-C59 and continue incubation for 48 hours. On day four, remove 166 microliters of medium from each well and add 166 microliters of fresh RPMI 1640 with insulin free B27 supplement, then incubate another 48 hours. On day six, remove 166 microliters of medium from each well and add 166 microliters of RPMI 1640 with B27 supplement.For this and all subsequent media changes, use B27 supplement with insulin, incubate for another 24 hours. On day seven, the cell culture is ready for pro epicardial differentiation. Remove 166 microliters of medium from each well and add 166 microliters of fresh RPMI 1640 containing B27 supplement and three micromolar cheer 99021.Then in incubate for one hour, after one hour remove the plate from the incubator, remove 166 microliters of medium from one side of each well and add 166 microliters of fresh RPMI 1640 containing B27 supplement continue incubation for another 48 hours. Repeat this process us every 48 hours until collection. Organoids are ready for analyses and experimentation on day 15 To transfer the whole organoids, cut the tip of a P200 pipette, five to 10 millimeters from the opening with a diameter of approximately two to three millimeters.Press the pipette plunger and insert the tip vertically into the round bottom well with the organoid. Take up approximately 100 to 200 microliters of medium enough to collect the organoids and transfer them to the target destination. Before differentiation EBS appear as blacks spherical masses the differentiation process starts on day zero with a Wnt pathway activation and growth factor addition for exactly 24 hours.Further the edit of Wnt C59 on day two results in enlargement of the organoid from approximately 200 micrometers to a maximum of one millimeter. The human heart organoids began beating as early as day six and 100%of the organoids showed visible beating by day 10. High magnification images of day seven organoid revealed that most hand one expressing cells were cardiomyocyte in origin and hand two were non myosite cells from second Heartfield, progenitor cells.RNA transcripts for both hand one and hand two were expressed from day three onwards in RNA sequencing data. The FHF markers were highly expressed during days three and 11 while the SF marker was more highly expressed after day 13. Immunofluorescence stain revealed the presence of various human heart cell type lineages that make up the human heart.Such as myocardial and epicardial tissue, endocardial cells, endothelial cells, and cardiac fibroblast. The markers expressing the above cell lineages were also observed in the RNA SAC gene expression profiles. Live calcium imaging of individual cells in whole organoids was used to measure the electrophysiological function of the organoids.Fluo-4 fluorescence intensity varied over time due to calcium entry exit from the cell revealing regular action potentials. Heat maps showing calcium intensities over a high magnification region of the organoid, show increased intensity due to calcium transients and individual cells. When attempting this protocol, keep in mind that the EBs and subsequent organoids are not attached to the bottom of the plate, and we'll move around with the removal in addition of media requiring attentive media changes.Organoids can be culture for longer periods of time introduced to maturation techniques, or even exposed to external stimuli, such as mechanical or electrical conditioning, and even stressors such as toxins. This technique allow as access to stages of human fetal heart development that are otherwise inaccessible in research, paving the way for new insights into heart development and disease etiology.

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Research

JoVE Journal

Biochemistry

Enrichment of Detergent-insoluble Protein Aggregates from Human Postmortem Brain

In this study, we describe an abbreviated single-step fractionation protocol for the enrichment of detergent-insoluble protein aggregates from human postmortem brain. The ionic detergent N-lauryl-sarcosine (sarkosyl) effectively solubilizes natively folded proteins in brain tissue allowing the enrichment of detergent-insoluble protein aggregates from a wide range of neurodegenerative proteinopathies, such as Alzheimer&#39;s disease (AD), Parkinson&#39;s disease and amyotrophic lateral sclerosis, and prion diseases. Human control and AD postmortem brain tissues were homogenized and sedimented by ultracentrifugation in the presence of sarkosyl to enrich detergent-insoluble protein aggregates including pathologic phosphorylated tau, the core component of neurofibrillary tangles in AD. Western blotting demonstrated the differential solubility of aggregated phosphorylated-tau and the detergent-soluble protein, Early Endosome Antigen 1 (EEA1) in control and AD brain. Proteomic analysis also revealed enrichment of &#946;-amyloid (A&#946;), tau, snRNP70 (U1-70K), and apolipoprotein E (APOE) in the sarkosyl-insoluble fractions of AD brain compared to those of control, consistent with previous tissue fractionation strategies. Thus, this simple enrichment protocol is ideal for a wide range of experimental applications ranging from Western blotting and functional protein co-aggregation assays to mass spectrometry-based proteomics.

An abbreviated fractionation protocol for the enrichment of detergent-insoluble protein aggregates from human postmortem brain is described.

In this study, we describe an abbreviated single-step fractionation protocol for the enrichment of detergent-insoluble protein aggregates from human ...

A Western Blotting Protocol for Small Numbers of Hematopoietic Stem Cells

Hematopoietic stem cells (HSCs) are rare cells, with the mouse bone marrow containing only ~25,000 phenotypic long term repopulating HSCs. A Western blotting protocol was optimized and suitable for the analysis of small numbers of HSCs (500 - 15,000 cells). Phenotypic HSCs were purified, accurately counted, and directly lysed in Laemmli sample buffer. Lysates containing equal numbers of cells were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and the blot was prepared and processed following standard Western blotting protocols. Using this protocol, 2,000 - 5,000 HSCs can be routinely analyzed, and in some cases data can be obtained from as few as 500 cells, compared to the 20,000 to 40,000 cells reported in most publications. This protocol should be generally applicable to other hematopoietic cells, and enables the routine analysis of small numbers of cells using standard laboratory procedures.

A standard Western blotting protocol was optimized for analyzing as few as 500 hematopoietic stem or progenitor cells. Optimization involves careful handling of the cell sample, limiting transfers between tubes, and directly lysing the cells in Laemmli sample buffer.

Hematopoietic stem cells (HSCs) are rare cells, with the mouse bone marrow containing only ~25,000 phenotypic long term repopulating HSCs. A Western ...

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Determination of the full-length structure of ribosome assembly factor Nsa1 from Saccharomyces cerevisiae (S. cerevisiae) is challenging because of the disordered and protease labile C-terminus of the protein. This manuscript describes the methods to purify recombinant Nsa1 from S. cerevisiae for structural analysis by both X-ray crystallography and SAXS. X-ray crystallography was utilized to solve the structure of the well-ordered N-terminal WD40 domain of Nsa1, and then SAXS was used to resolve the structure of the C-terminus of Nsa1 in solution. Solution scattering data was collected from full-length Nsa1 in solution. The theoretical scattering amplitudes were calculated from the high-resolution crystal structure of the WD40 domain, and then a combination of rigid body and ab initio modeling revealed the C-terminus of Nsa1. Through this hybrid approach the quaternary structure of the entire protein was reconstructed. The methods presented here should be generally applicable for the hybrid structural determination of other proteins composed of a mix of structured and unstructured domains.

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

This method describes the cloning, expression, and purification of recombinant Nsa1 for structural determination by X-ray crystallography and small-angle X-ray scattering (SAXS), and is applicable for the hybrid structural analysis of other proteins containing both ordered and disordered domains.

Determination of the full-length structure of ribosome assembly factor Nsa1 from Saccharomyces cerevisiae (S. cerevisiae) is challenging because of the ...

Polysome Profiling in Leishmania, Human Cells and Mouse Testis

Proper protein expression at the right time and in the right amounts is the basis of normal cell function and survival in a fast-changing environment. For a long time, the gene expression studies were dominated by research on the transcriptional level. However, the steady-state levels of mRNAs do not correlate well with protein production, and the translatability of mRNAs varies greatly depending on the conditions. In some organisms, like the parasite Leishmania, the protein expression is regulated mostly at the translational level. Recent studies demonstrated that protein translation dysregulation is associated with cancer, metabolic, neurodegenerative and other human diseases. Polysome profiling is a powerful method to study protein translation regulation. It allows to measure the translational status of individual mRNAs or examine translation on a genome-wide scale. The basis of this technique is the separation of polysomes, ribosomes, their subunits and free mRNAs during centrifugation of a cytoplasmic lysate through a sucrose gradient. Here, we present a universal polysome profiling protocol used on three different models - parasite Leishmania major, cultured human cells and animal tissues. Leishmania cells freely grow in suspension and cultured human cells grow in adherent monolayer, while mouse testis represents an animal tissue sample. Thus, the technique is adapted to all of these sources. The protocol for the analysis of polysomal fractions includes detection of individual mRNA levels by RT-qPCR, proteins by Western blot and analysis of ribosomal RNAs by electrophoresis. The method can be further extended by examination of mRNAs association with the ribosome on a transcriptome level by deep RNA-seq and analysis of ribosome-associated proteins by mass spectroscopy of the fractions. The method can be easily adjusted to other biological models.

Polysome Profiling in Leishmania, Human Cells and Mouse Testis

The overall goal of polysome profiling technique is analysis of translational activity of individual mRNAs or transcriptome mRNAs during protein synthesis. The method is important for studies of protein synthesis regulation, translation activation and repression in health and multiple human diseases.

Proper protein expression at the right time and in the right amounts is the basis of normal cell function and survival in a fast-changing environment. For ...

Dynamic Proteomic and miRNA Analysis of Polysomes from Isolated Mouse Heart After Langendorff Perfusion

Studies in dynamic changes in protein translation require specialized methods. Here we examined changes in newly-synthesized proteins in response to ischemia and reperfusion using the isolated perfused mouse heart coupled with polysome profiling. To further understand the dynamic changes in protein translation, we characterized the mRNAs that were loaded with cytosolic ribosomes (polyribosomes or polysomes) and also recovered mitochondrial polysomes and compared mRNA and protein distribution in the high-efficiency fractions (numerous ribosomes attached to mRNA), low-efficiency (fewer ribosomes attached) which also included mitochondrial polysomes, and the non-translating fractions. miRNAs can also associate with mRNAs that are being translated, thereby reducing the efficiency of translation, we examined the distribution of miRNAs across the fractions. The distribution of mRNAs, miRNAs, and proteins was examined under basal perfused conditions, at the end of 30 min of global no-flow ischemia, and after 30 min of reperfusion. Here we present the methods used to accomplish this analysis&#8212;in particular, the approach to optimization of protein extraction from the sucrose gradient, as this has not been described before&#8212;and provide some representative results.

Here we present a protocol to perform polysome profiling on the isolated perfused mouse heart. We describe methods for heart perfusion, polysome profiling, and analysis of the polysome fractions with respect to mRNAs, miRNAs, and the polysome proteome.

Studies in dynamic changes in protein translation require specialized methods. Here we examined changes in newly-synthesized proteins in response to ...

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

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

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

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

Extracellular Glucose Depletion as an Indirect Measure of Glucose Uptake in Cells and Tissues Ex Vivo

The ongoing worldwide epidemic of diabetes increases the demand for the identification of environmental, nutritional, endocrine, genetic, and epigenetic factors affecting glucose uptake. The measurement of intracellular fluorescence is a widely used method to test the uptake of fluorescently-labeled glucose (FD-glucose) in cells in vitro, or for imaging glucose-consuming tissues in vivo. This assay assesses glucose uptake at a chosen time point. The intracellular analysis assumes that the metabolism of FD-glucose is slower than that of endogenous glucose, which participates in catabolic and anabolic reactions and signaling. However, dynamic glucose metabolism also alters uptake mechanisms, which would require kinetic measurements of glucose uptake in response to different factors. This article describes a method for measuring extracellular FD-glucose depletion and validates its correlation with intracellular FD-glucose uptake in cells and tissues ex vivo. Extracellular glucose depletion may be potentially applicable for high-throughput kinetic and dose-dependent studies, as well as identifying compounds with glycemic activity and their tissue-specific effects.

Extracellular Glucose Depletion as an Indirect Measure of Glucose Uptake in Cells and Tissues Ex Vivo

Extracellular depletion of fluorescently labeled glucose correlates with glucose uptake and could be used for high-throughput screening of glucose uptake in excised organs and cell cultures.

The ongoing worldwide epidemic of diabetes increases the demand for the identification of environmental, nutritional, endocrine, genetic, and epigenetic ...

Human Mesenchymal Stem Cell Processing for Clinical Applications Using a Closed Semi-Automated Workflow

Human mesenchymal stem cells (hMSCs) are currently being explored as a promising cell-based therapeutic modality for various diseases, with more market approvals for clinical use expected over the next few years. To facilitate this transition, addressing the bottlenecks of scale, lot-to-lot reproducibility, cost, regulatory compliance, and quality control is critical. These challenges can be addressed by closing the process and adopting automated manufacturing platforms. In this study, we developed a closed and semi-automated process for passaging and harvesting Wharton's jelly (WJ)-derived hMSCs (WJ-hMSCs) from multi-layered flasks using counterflow centrifugation. The WJ-hMSCs were expanded using regulatory compliant serum-free xeno-free (SFM XF) medium, and they showed comparable cell proliferation (population doubling) and morphology to WJ-hMSCs expanded in classic serum-containing media. Our closed semi-automated harvesting protocol demonstrated high cell recovery (~98%) and viability (~99%). The cells washed and concentrated using counterflow centrifugation maintained WJ-hMSC surface marker expression, colony-forming units (CFU-F), trilineage differentiation potential, and cytokine secretion profiles. The semi-automated cell harvesting protocol developed in the study can be easily applied for the small- to medium-scale processing of various adherent and suspension cells by directly connecting to different cell expansion platforms to perform volume reduction, washing, and harvesting with a low output volume.

Here, we present a protocol to harvest adherent cells from multi-layered flasks in a closed semi-automated manner using a counterflow centrifugation system. This protocol can be applied for harvesting both adherent and suspension cells from other cell expansion platforms with few modifications to the existing steps.

Human mesenchymal stem cells (hMSCs) are currently being explored as a promising cell-based therapeutic modality for various diseases, with more market ...

Isolating Small Extracellular Vesicles and Extracting Their Peptidome

Identification of Peptides of Small Extracellular Vesicles from Bone Marrow-Derived Macrophages

Small extracellular vesicles (sEVs) are typically secreted by the exocytosis of multivesicular bodies (MVBs). These nanovesicles with a diameter of &lt;200 nm are present in various body fluids. These sEVs regulate various biological processes such as gene transcription and translation, cell proliferation and survival, immunity and inflammation through their cargos, such as proteins, DNA, RNA, and metabolites. Currently, various techniques have been developed for sEVs isolation. Among them, the ultracentrifugation-based method is considered the gold standard and is widely used for sEVs isolation. The peptides are naturally biomacromolecules with less than 50 amino acids in length. These peptides participate in a variety of biological processes with biological activity, such as hormones, neurotransmitters, and cell growth factors. The peptidome is intended to systematically analyze endogenous peptides in specific biological samples by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Here, we introduced a protocol to isolate sEVs by differential ultracentrifugation and extracted peptidome for identification by LC-MS/MS. This method identified hundreds of sEVs-derived peptides from bone marrow-derived macrophages.

Author Spotlight: Peptidome Extraction from Small Extracellular Vesicles Isolated from Bone Marrow-Derived Macrophages 

This protocol describes a procedure to isolate small extracellular vesicles from macrophages by differential ultracentrifugation and extract the peptidome for identification by mass spectrometry.

Small extracellular vesicles (sEVs) are typically secreted by the exocytosis of multivesicular bodies (MVBs). These nanovesicles with a diameter of ...

Locus-Specific Chromatin Isolation from Yeast Cells

Single-Copy Gene Locus Chromatin Purification in Saccharomyces cerevisiae

The basic organizational unit of eukaryotic chromatin is the nucleosome core particle (NCP), which comprises DNA wrapped ~1.7 times around a histone octamer. Chromatin is defined as the entity of NCPs and numerous other protein complexes, including transcription factors, chromatin remodeling and modifying enzymes. It is still unclear how these protein-DNA interactions are orchestrated at the level of specific genomic loci during different stages of the cell cycle. This is mainly due to the current technical limitations, which make it challenging to obtain precise measurements of such dynamic interactions. Here, we describe an improved method combining site-specific recombination with an efficient single-step affinity purification protocol to isolate a single-copy gene locus of interest in its native chromatin state. The method allows for the robust enrichment of the target locus over genomic chromatin, making this technique an effective strategy for identifying and quantifying protein interactions in an unbiased and systematic manner, for example by mass spectrometry. Further to such compositional analyses, native chromatin purified by this method likely reflects the in vivo situation regarding nucleosome positioning and histone modifications and is, therefore, amenable to further structural and biochemical analyses of chromatin derived from virtually any genomic locus in yeast.

Author Spotlight: Advancing Chromatin Research and Overcoming Limitations with a High-Enrichment Locus-Specific Chromatin Isolation Protocol 

This protocol presents a locus-specific chromatin isolation method based on site-specific recombination to purify a single-copy gene locus of interest in its native chromatin context from budding yeast, Saccharomyces cerevisiae.

The basic organizational unit of eukaryotic chromatin is the nucleosome core particle (NCP), which comprises DNA wrapped ~1.7 times around a histone ...