assessing the impact of spheroid formation methods in 3d cell culture systems using live cell fluorescence lifetime imaging microscopy (flim)

Multicellular Spheroid Formation for FLIM-Based Metabolic and Hypoxia Analysis

Multicellular spheroids represent a group of 3D tissue models obtained by the self-aggregation of cells and exhibiting a spherical shape. They are widely used to mimic cell-cell and cell-matrix interaction in vitro and to reproduce&#160;a 3D context within a multitude of cancer and stem cell-derived constructs. Several techniques are employed to reduce cell attachment and promote the aggregation. These include the hanging-drop method relying on the surface tension1; cell attachment repelling methods such as ultra-low attachment plates, micro-molds, and microwells2,3; acoustic wave-based approach4; flow-induced aggregation methods (spinner flasks, bioreactor, and microfluidic devices)5; magnetic particles-assisted formation6 and use of the aggregation-promoting synthetic and ECM-based matrices and scaffolds7,8,9.
In cancer research, development, and validation of new drug therapies, spheroids are an attractive model due to their ability to recapitulate the spatial diffusion-limited gradients of nutrients, waste products, and O2, often leading to the formation of a necrotic core, typical to the solid tumors10,11. These more reliable and sophisticated in vitro models challenge the need for extensive use of animal models (Food and Drug Administration [FDA] Modernization Act 2.012), according to the 3Rs principle of animal research (replacement, reduction, and refinement). In addition to cancer, spheroids find their application in stem cell research. For instance, pluripotent stem cells have the capacity to form embryoid bodies (EB), which can be used for the differentiation of induced pluripotent stem cells (iPSCs) towards specialized cell types that are challenging to obtain directly from patients, such as neural precursor cells13 or ovarian granulosa cells13,14. Furthermore, the formation of an EB is often the first step in the development of more complex organoid models, e.g., neural15, retinal16, cardiac17, liver18, stomach19, and intestinal organoids20. Factors including size, reproducibility, throughput, and downstream applications should be considered when choosing an appropriate spheroid formation method for the experiments.
The increased complexity of 3D culture can lead to higher variability compared to 2D culture. Factors such as nutrient composition21, media evaporation22, viscosity23, pH control24, spheroid formation method, and even the time in the culture25,26 can result in obtaining spheroids of varying morphology, sizes, viability, and different chemoresistance27,28. Recent research demonstrated that spheroid oxygen gradients are not always static and are affected by the formation method, spheroid size, and extracellular viscosity, affecting the spheroid heterogeneity29. To improve reproducibility and data accessibility on spheroids, the MISpheroID knowledge base has been developed26, identifying cell line, culture medium, formation method, and spheroids size as the minimal information for a reproducible result. Therefore, a detailed comparison was made of multiple high-throughput (SphericalPlate 5D, lab-made micromolds, and Microtissue molds) and low attachment methods (i.e., Biofloat and Lipidure-coated 96-well plates, both scaffold-free and scaffold-based) (Figure 1 and Table 1), including the well size (given an estimation of the maximum spheroid size), consumables used, preparation time and the possibility of monitoring spheroids without transporting them to microscopy dishes. The latter enables long-term studies, whereas spheroids produced with high-throughput methods often result in endpoint experiments. All methods except for the grids of the 5DspheriPlate do not bring unwanted autofluorescence, hereby enabling their direct use in microscopy.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/66845/66845fig01.jpg" /> 
Figure 1: Spheroid formation methods explained. High-throughput methods such as the SphericalPlate 5D, which has integrated patented microwells in the plate, while the lab-produced micromolds and the MicroTissue molds use stamps to make multiple microwells in agarose (blue). Low-attachment plates such as Lipidure (Amsbio) and Biofloat (Sarstedt) use a non-adherent coating inhibiting cell-surface adhesion and promoting cell self-aggregation. <a href="https://www.jove.com/files/ftp_upload/66845/66845fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td></td>
			<td>5D SpheriPlate</td>
			<td>Self-produced micromolds</td>
			<td>Microtissue</td>
			<td>Low attachment methods</td>
		</tr>
		<tr>
			<td>Number of spheroids/well&#160;</td>
			<td>750</td>
			<td>1589</td>
			<td>81</td>
			<td>1</td>
		</tr>
		<tr>
			<td>Diameter well</td>
			<td>90 &#181;m</td>
			<td>400 &#181;m</td>
			<td>800 &#181;m</td>
			<td>1 mm</td>
		</tr>
		<tr>
			<td>Culture volume</td>
			<td>1 mL</td>
			<td>5 mL</td>
			<td>1 mL</td>
			<td>200 &#181;L</td>
		</tr>
		<tr>
			<td>Other consumables</td>
			<td>/</td>
			<td>7 mL of 3% agarose</td>
			<td>500 &#181;L of 2% agarose</td>
			<td>/ *</td>
		</tr>
		<tr>
			<td>Preparation time</td>
			<td>10 min</td>
			<td>2 h + 3 days media adaptation</td>
			<td>0.5 h + 15 min media adaptation</td>
			<td>10&#8211;30 min + 1 h drying</td>
		</tr>
		<tr>
			<td>Monitoring</td>
			<td>Yes</td>
			<td>No**</td>
			<td>Yes</td>
			<td>Yes</td>
		</tr>
		<tr>
			<td>Autofluorescent</td>
			<td>Yes</td>
			<td>No</td>
			<td>No</td>
			<td>No</td>
		</tr>
		<tr>
			<td>Reusable</td>
			<td>No</td>
			<td>Yes</td>
			<td>Yes</td>
			<td>No**</td>
		</tr>
		<tr>
			<td rowspan="2">Cost</td>
			<td rowspan="2">&#8364;&#8364;&#160;</td>
			<td rowspan="2">&#8364;</td>
			<td rowspan="2">&#8364;&#8364;&#8364;&#8364;</td>
			<td>&#8364;&#8364;&#8364;&#8364;: Coating and Matrigel</td>
		</tr>
		<tr>
			<td>&#8364;&#8364;: Commercial 96-well plate</td>
		</tr>
		<tr>
			<td colspan="3">*Some cell lines need addition of&#160; ECM (i.e. 2%&#8211;5% Matrigel) to form compact spheroids.&#160;</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td colspan="5">**The coating is reusable until depleted. However, each plate will consume a small amount of media and dust can accumulate over time. Filter sterilization is regularly needed.&#160;</td>
		</tr>
	</tbody>
</table>
Table 1: Comparison of multiple spheroid formation methods29. &#34;Monitoring&#34;: the ability to monitor spheroid without the need for transfer to a microscopy dish. &#8364;: 0-50&#8364;, &#8364;&#8364;: 50-150&#8364; , &#8364;&#8364;&#8364;: 150-500&#8364; , &#8364;&#8364;&#8364;&#8364;: &#62;500&#8364;
Fluorescence microscopy enables direct monitoring of the key biological aspects within spheroids, including cell death, viability, proliferation, metabolism, viscosity, and even mechanical properties30. Fluorescence lifetime imaging microscopy (FLIM) provides an additional quantitative dimension for studying fluorescent probe interactions within their (micro)environment31,32,33,34, allowing resolving the overlapping emission spectra according to different emission lifetimes35,36 and probing cell metabolism based on intrinsic cellular autofluorescence. Thus, such widespread cellular autofluorescent compounds as nicotinamide adenine dinucleotide phosphate (NAD(P)H), flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), protoporphyrin IX, and others can be measured with one- and two-photon FLIM and serve as intrinsic &#39;sensors&#39; of glucose catabolism, oxidative phosphorylation (OxPhos) and provide a general overview of the cell redox state. NAD(P)H exists in free cytoplasmic, or in protein-bound mitochondrial forms37,38. Similarly, the oxidized state of FAD is fluorescent with a longer lifetime of the free form. NAD(P)H and FAD microscopies usually involve two-photon excited FLIM, aiming at preventing sample photodamage39. Frequently, &#39;optical metabolic imaging&#39; FLIM can be combined with the use of dye-based probes, genetically encoded biosensors, phosphorescence lifetime imaging microscopy (PLIM), and ratiometric intensity-based measurements in order to provide a more complete picture of spheroid or organoid metabolism, oxygenation, proliferation and cell viability29,30,31. In addition, FLIM can also be combined with F&#246;rster resonance energy transfer (FRET) method to measure the lifetime variation of the donor fluorophore when in close contact with the acceptor to investigate the binding of a drug with its target domain33,40,41.
The acquired FLIM images are typically analyzed to calculate the lifetime pixel-by-pixel. Currently, there are at least 3 common strategies used to obtain fluorescence lifetime: semi-quantitative &#39;fast FLIM&#39;42 (sometimes referred to as &#39;tau sense&#39;43,44), decay curve fitting, using one-, two- or three-exponential fitting, and &#39;fitting-free&#39; approach with phasor transformation and phasor plot analysis. Depending on the vendor, either provided (LAS X, Symphotime, SPCImage, etc.) or open-source software (e.g., FLIMfit45, FLIMJ46, or others47) can be used to handle measured FLIM data. Typically, vendor-provided software is useful for preliminary data analysis, while open-source solutions can provide for more accurate studies using, e.g., phasor plots and 3D visualization.
Despite the usefulness and attractiveness of FLIM as a method for studying spheroids, very few experimental protocols are available, and there is a general lack of knowledge in choosing the most appropriate formation method for successful live multiparametric microscopy experiments involving FLIM. Here, a detailed comparison of commonly used spheroid formation protocols is presented based on their morphology, viability, and oxygenation with the recently validated and characterized far-red and near-infra-red (NIR) oxygen-sensing nanosensor (MMIR1). The cationic nanoparticle is impregnated with two reporter dyes, the reference O2-insensitive aza-BODIPY (excitation 650 nm, emission 675 nm) and the NIR O2-sensitive metalloporphyrin, PtTPTBPF (excitation 620 nm, emission 760 nm). The MMIR1 enables real-time analysis of oxygen gradients on a conventional fluorescence microscope (using ratiometric analysis) or phosphorescence lifetime microscope (PLIM) without introducing cellular toxicity and allowing for stable signals, long-term monitoring, and multiplexing25,29. Depending on the need to stain with dyes or nanosensors, spheroid throughput, or cell type, the most appropriate formation protocol can be chosen. Since the studies of spheroids viability and oxygenation are relevant for studies of cancer and stem cell-derived spheroids, the presented protocols also include examples and expected typical results of NAD(P)H-FLIM and&#160;FAD-FLIM with these models. The presented imaging and analysis pipelines target the most popular time-correlated single photon counting-based FLIM microscopy platforms.

Author Spotlight: Standardizing Spheroid Formation Methods for Metabolic and Oxygenation Analysis Using Fluorescence Lifetime Imaging Microscopy

Production and Multi-Parameter Live Cell Fluorescence Lifetime Imaging Microscopy (FLIM) of Multicellular Spheroids

In this work, we present and compare spheroid formation methods that can be used for analysis of cell metabolism and oxygen distribution using live cell microscopy. In recent years, fluorescence lifetime imaging microscopy has been extensively used to investigate metabolic biomarkers like NADPH and FAD in live cells, and several fluorescent nanoparticles have been developed to multiplex such measurements with imaging of cell and tissue oxygenation. Multicellular spheroids, organoids, and organ-on-a-chip can replicate a complex, in-vivo-like microenvironment, minimizing the need in animal research.For spheroid production, we show different formation methods, can span from low to high throughput. They also highlight their optical accessibility, compatibility with fluorescence lifetime imaging microscope, and the possibility of including extracellular matrix components. So, even though 3D in vitro models provide better context in comparison to 2D cultures, their high variability, low reproducibility, and incomplete experimental reporting remain a problem.Parameters such as the spheroid size, the nutrient composition, the extracellular viscosity, and even spheroid formation methods can all lead to increased cellular heterogeneity. With this protocol, we aim to harmonize and standardize the spheroid production methods, highlighting key aspects important for life-continuous and multiparametric analysis of spheroids using FLIM microscopy.

Assessing the Impact of Spheroid Formation Methods in 3D Cell Culture Systems Using Live Cell Fluorescence Lifetime Imaging Microscopy (FLIM)

To begin, place the prewarmed imaging medium and sterile microscopy dishes with coated or non-coated cover glass surfaces on a working platform. After removing the medium surrounding the agarose mold, carefully resuspend the content of the molds in 190 microliters media before transferring floating spheroids into a two milliliter vial. For spheroids in a low-attachment plate, transfer spheroids one by one from individual wells to a vial.Allow the spheroids to settle down at the bottom of the vial for five minutes, forming a visible pellet. Remove the media from the vial, leaving spheroids undisturbed, and gently resuspend them in a sufficient amount of fresh McCoy's 5A medium. Now, transfer an equal volume of spheroid suspension per well of the microscopy dish.Incubate spheroid for 1 to 2 hours at 37 degrees Celsius in a carbon dioxide incubator. Add a fluorescence probe to a known volume of spheroid suspension and continue incubation for 1 hour at 37 degrees Celsius. After incubation, exchange the media containing fluorescent probes with a necessary volume of imaging media.Start the microscope control software and initialize the stage calibration. Then, choose the required objective. Choose the Open project window and click Create a New Project.Then, right click on the newly created project and select the Rename option in the dropdown menu. Give a standard name to the research project file. Open the Acquisition window.Set the pulse white light laser excitation wavelength and the required range of hybrid or resonance scanning detectors. Then, choose line or frame types of scan. In the Acquisition window, select FLIM mode to perform imaging combined with photon counting.Then, choose the white light laser pulse repetition rate. Start the preview imaging using Fast Live mode and adjust the fine focus of the imaging object on a section of interest. By looking at the pixel intensity histogram, adjust the appropriate laser intensity pinhole size and resolution.While in Fast Live, set the coordinates and scan direction and attribute them to begin and end in the Z-Stack window. Choose a z-step size or number of steps. Once all necessary settings are applied, start imaging.Give the image an appropriate name and save the imaging project. Different formation methods resulted in varying spheroid sizes. HCT116 spheroids in low attachment plates were significantly larger after five days compared to high throughput methods.Low attachment methods led to the evident development of a necrotic core detected by the propidium iodide staining. In contrast, spheroids generated with other methods demonstrated the diffused distribution of dead cells across the spheroid body. Oxygenation in HCT116 spheroids produced by different methods showed more oxygenated spheroid with the microtissue and lab-made micromolds than the Sphericalplate 5D.Spheroid oxygenation of Sphericalplate 5D spheroids showed lower oxygenation compared to microtissue and lab-made micromolds. Phasor analysis of HCT116 spheroids made using low-attachment plates reveals the presence of glycolytic and non-glycolytic cores via two-photon NADPH-FLIM.

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