Presented here is a protocol for cell culture on silicon nitride membranes and plunge-freezing prior to X-ray fluorescence imaging with a synchrotron cryogenic X-ray nanoprobe. When only room temperature nano-analysis is provided, the frozen samples can be further freeze-dried. These are critical steps to obtain information on the intracellular elemental composition.
Very little is known about the distribution of metal ions at the subcellular level. However, those chemical elements have essential regulatory functions and their disturbed homeostasis is involved in various diseases. State-of-the-art synchrotron X-ray fluorescence nanoprobes provide the required sensitivity and spatial resolution to elucidate the two-dimensional (2D) and three-dimensional (3D) distribution and concentration of metals inside entire cells at the organelle level. This opens new exciting scientific fields of investigation on the role of metals in the physiopathology of the cell. The cellular preparation is a key and often complex procedure, particularly for basic analysis. Although X-ray fluorescence techniques are now widespread and various preparation methods have been used, very few studies have investigated the preservation of the elemental content of cells at best, and no stepwise detailed protocol for the cryopreparation of adherent cells for X-ray fluorescence nanoprobes has been released so far. This is a description of a protocol that provides the stepwise cellular preparation for fast cryofixation to enable synchrotron X-ray fluorescence nano-analysis of cells in a frozen hydrated state when a cryogenic environment and transfer is available. In case nano-analysis has to be performed at room temperature, an additional procedure for freeze-drying the cryofixed adherent cellular preparation is provided. The proposed protocols have been successfully used in previous works, most recently in studying the 2D and 3D intracellular distribution of an organometallic compound in breast cancer cells.
Newly designed synchrotron X-ray fluorescence (SR-XRF) nanoprobes allow visualization of the subcellular distribution of elements in a fully quantitative manner. As an example, this analytical capability allows investigation of the uptake of nanoparticles1 or organometallic molecules such as osmium-based complexes2, providing insight into the intracellular uptake of metal-based molecules with potent anticancer properties. As a multielement technique, SR-XRF3 with a nanoprobe provides a way to simultaneously quantify and localize intracellularly most biologically important elements, including phosphorus, sulfur, potassium, calcium, iron, copper, and zinc. Indeed, the use of hard X-rays provides large penetration depth to image whole frozen-hydrated cells in a label-free fashion. Furthermore, providing access to the K-edge of most elements of interest, the X-ray fluorescence is excited most efficiently. The use of cryogenic approaches allows reduction of radiation damage and optimization of the preservation of the cell structure and elemental distribution.
Most available spatially resolved analytical techniques to study metals in cells are surface techniques requiring very thin and flat sections of cells to be produced. This mainly encompasses scanning transmission electron microscopy with energy-dispersive X-ray analysis (STEM–EDX), energy-filtered transmission electron microscopy (EF-TEM), and nanoscale secondary ion mass spectrometry (nanoSIMS). The latter cannot be performed on frozen, hydrated cell sections while cryo-analysis can be done with electron microscopy with unsurpassed spatial resolution but poor elemental sensitivity. Particle-induced X-ray emission (PIXE) has allowed the study of elemental distributions in whole cells. It has the advantage of being fully quantitative with a fair elemental sensitivity at the micron scale and even at submicron resolution4, but suffers from radiation damage and lack of cryogenic capabilities to study frozen-hydrated cells. All these analytical techniques complement each another in the elemental imaging of cells, but for all techniques the sample preparation procedure is a crucial step. It should be kept simple to limit possible contamination as well as elemental redistribution and/or leakage to obtain meaningful results. As demonstrated in electron microscopy, a cryogenic workflow, including cryo-immobilization of the cell and cryotransfer to a cryoscanning stage, allows an optimal elemental preservation at subcellular levels as close as possible to the native state5,6,7,8,9,10. This understanding has been successfully implemented into the development of synchrotron cryo-soft X-ray microscopy (e.g., full field microscopes and scanning microscopes) to produce ultrastructural imaging of entire frozen-hydrated cells in 2D or 3D. Various cryogenic workflows were developed11 for soft X-ray microscopes at Beamline 2.1 (XM-2) of the Advanced Light Source at Lawrence Berkeley National Laboratory12, beamline U41-XM at the electron storage ring BESSY II (Germany)13, beamline MISTRAL of the ALBA light source (Spain)14, and at Beamline B24 of the Diamond light source15, among others. A similar workflow was recently shown to be the most reliable preparation and preservation method for intracellular elemental analysis using X-ray microprobes16,17.
Although X-ray nanoprobe techniques are starting to be widely used for cellular elemental analysis, particularly with the advent of cryogenic SR-XRF capabilities, no stepwise protocol has been disseminated so far to the research community. Here, a detailed procedure is provided to prepare cryofixed adherent cells cultured as monolayers on silicon nitride membranes to be analyzed under cryogenic conditions. A freeze-drying step to be applied after the protocol in case the X-ray analysis must be performed at room temperature is also provided. While the proposed protocol has been successfully used with human breast cancer cells MD-MB-2312 and the freeze-drying was demonstrated among others on mouse neurons18,20,21, it can be easily extended to various types of human or animal cells.
Experimental procedures were approved by the animal care committee of the CEA’s Life Sciences Division (CETEA, A14-006). They were conducted in compliance with the French legislation and the European Community Council Directive of 24 November 1986 (86/609/EEC).
1. Silicon nitride (Si3N4) membrane support preparation
NOTE: Because the membrane is fragile and delicate, its support (200 µm thick silicon frame) has to be handled gently, ideally with a thin carbon tweezers or Dumont Tweezers #5, Straight Self-closing fine tips. This protocol used silicon nitride membranes with a frame of 5 mm x 5 mm and a membrane size of 1.5 mm x 1.5 mm. The membrane should be prepared roughly 12 h before starting the experiment (i.e., cell seeding). Membranes can be prepared at the end of the day and left drying overnight under a Class II laminar flow hood so they are ready to use the next morning. A silicon frame thickness of 200 µm is standard for most companies that sell silicon nitride windows. If the product used in this protocol is not available, a membrane size in the range of 0.5−1.5 mm can be used with a standard frame size of 5 mm x 5 mm. The larger membrane size is preferred when X-ray tomography will be used. TEM grid type silicon nitride windows with a membrane size of 0.5 mm and a thickness of 50 nm can also be used.
2. Cell seeding
3. Treatment or medium change
4. Cryo-immobilization of the cellular preparation by plunge-freezing
NOTE: At the end of the required incubation time, in the presence or absence of treatment, the cells have to be carefully rinsed and cryofixed. Around 30 min before starting to rinse and blot the cellular preparation prior to plunge-freezing, first set-up and cool down the automatic plunge freezer machine. As you manipulate cryogens, the use of appropriate cryogenic gloves, safety glasses, closed shoes, and a laboratory coat are required. Liquid nitrogen must be transported in appropriate Dewars, and the working place should be sufficiently ventilated with the presence of an oxygen monitor. Ideally, a low hygrometry level of 20−30% helps to limit ice contamination of the materials, Dewars, and cryogens, that is detrimental for the vitrification of the samples (i.e., an amorphous ice layer). Ideally, depending on the experience level of the researcher, up to 10−12 samples for a single session can be prepared using the same secondary cryogen liquid ethane cup for vitrification. Between sessions, the automatic plunge freezer requires a 1 h automatic bake-out procedure. Ideally, samples should be processed with identical incubation conditions. Still, controls can be processed first, followed by the samples with a particular treatment condition.
NOTE: For plunge-freezing the following steps apply both to MDA-MB-231 or HN cells.
5. Freeze-drying of plunge-frozen cells cultured on silicon nitride membranes
NOTE: For freeze-drying, the following steps apply to both MDA-MB-231 and HN cells. To cool down the freeze dryer, you will need to wait around 40 min to 1 h.
A typical optical video microscope view of frozen hydrated MDA-MB-231 cells that were sub-cultured onto a poly-L-lysine coated Si3N4 membrane support is shown in Figure 7A. The optical view of the sample in the vacuum chamber was obtained in reflection mode using the dedicated online video microscope of the ID16A beamline of the ESRF22. While electron or soft X-ray microscopy requires the ice layer embedding the cell to be as thin as possible (typically <0.5 µm), hard X-rays (>10 keV) have the advantage of a much higher penetration depth and lower dose deposition. The ice thickness can therefore be larger, typically <10 µm including the cell so that the ice embedding the cell is a few µm in thickness. This can be estimated through the measured X-ray intensity in transmission compared to the intensity without the sample, taking into account the absorption of the 500 nm thick Si3N4 membrane. This ice thickness can be achieved through manual blotting as described in the present protocol. In the Newton rings region, the ice thickness can be even thinner (not measured).
The X-ray fluorescence elemental mapping of the frozen hydrated cell is shown in Figure 7B with the representative distributions of physiological elements such as potassium (K), sulfur (S), and zinc (Zn). These maps represent the elemental areal mass (i.e., elemental projected mass). While not done in the present case, such maps can be normalized through X-ray propagation-based phase contrast imaging that provides the estimation of the sample projected mass23. As reported by many studies, the highly diffusible K ion in cells preserved in their near-native state was assumed to be homogeneously distributed throughout the entire cell23,24,16. As shown in the 2D X-ray fluorescence elemental images in Figure 7B, the tightly bound element S was evenly distributed within the cell, similarly to K, and represents a good estimate of the cellular mass profile. The Zn distribution had a higher signal in the nucleus than in the cytosol and clearly outlined the nucleus. It can be noted that small Zn-enriched regions can be detected at the spatial resolution (50 nm) in the nuclear region.
The existing X-ray nanoprobes or the ones to be built do not necessarily accommodate cryogenic capabilities. In this case, the best alternative to get X-ray fluorescence images of cells at sub-100 nm spatial resolutions is to perform a freeze-drying procedure described in this protocol after plunge-freezing of the cell. Figure 8A shows a typical bright field microscopy view of resultant freeze-dried primary mouse hippocampal neurons directly cultured on the Si3N4 membrane. In this case, if stored in a clean desiccated chamber, the samples can be prepared 1−2 weeks in advance and be observed with an ordinary upright optical microscope for registration of regions of interest. Care should be taken to prevent exposure to ambient humidity as it may be captured by the freeze-dried sample and lead to damage under the X-ray nanobeam. This procedure was applied successfully to very sensitive cells (i.e., neuronal cells) and even better results were obtained with other more robust types of cells, such as cancer cells. As for plunge-frozen cells, the X-ray fluorescence images of K, S, and Zn on the entire freeze-dried cell display are similar to the ones described above. They are representative of the elemental distributions to be found in various types of freeze-dried cells at 50−100 nm spatial resolution. While freeze-drying whole cells is an alternative to preserve elemental integrity, it is at the expense of a perfect preservation of the cell morphology16, particularly cell membranes.
Figure 1: Typical sample support for X-ray fluorescence nano-analysis. A Si3N4 membrane support in its protective capsule. This type of substrate can be used both for room temperature analysis (plunge-freeze cellular preparation followed by low temperature and low vacuum freeze-drying process) or for cryogenic X-ray fluorescence analysis. Please click here to view a larger version of this figure.
Figure 2: Schematic view of the silicon nitride windows after cell seeding. The cells are cultured directly onto the poly-L-lysine coated flat surface of the Si3N4 membrane support. Sometimes air bubbles can be trapped in the backside cavity of the Si3N4 membrane support and have to be removed as described in the protocol. Please click here to view a larger version of this figure.
Figure 3: In-house developed 3D printed cryo-box for long-term storage of plunge frozen Si3N4 membrane supports in liquid nitrogen Dewar. (A) Cryo-box disassembled with the container and the caps (lower part) and (B) the assembled cryo-box with locked caps. The caps can be manipulated with the tweezers, opening or locking by rotation. A detailed plan for 3D printing is available upon request from ESRF ID16A. The design has been made to accommodate silicon nitride TEM grids. Please click here to view a larger version of this figure.
Figure 4: Blotting of cells cultured on Si3N4. Prior to plunge-freezing the cell monolayer cultured onto a Si3N4 membrane needs to be rinsed in ammonium acetate solution (A) and carefully manually blotted using filter paper (B). Please click here to view a larger version of this figure.
Figure 5: Automatic plunge-freezing EM-GP machine. (A) The automatic plunge freezer. (B) Environmental chamber with the tweezers locked in. (C) The ethane cup covered with the Leica liquefier connected to an ethane bottle. (D) The plunge-freezing enclosure showing the black cup full of liquified ethane and the cryo-box for further storage in LN2 of the vitrified Si3N4 membranes. Please click here to view a larger version of this figure.
Figure 6: Sample cryotransfer assembly for freeze-drying procedure. (A) The first brass recipient for Si3N4 membranes is mounted on top of the sample transfer holder provided by the freeze dryer supplier. (B) and (C) show that the second flat brass disc is used as a cover and acts as a cold trap enclosure to be inserted in the vacuum enclosure of the freeze dryer. (D) The full assembly with the spring-loaded transfer rod. (E) The sample holder carrying the vitrified cellular preparation grown on the Si3N4 membrane must be further inserted in the LN2-cooled freeze dryer. All the steps for mounting the assembly are done in LN2 in a Styrofoam box. For clarity, all the images were produced in the absence of LN2. Please click here to view a larger version of this figure.
Figure 7: Cryo-X-ray fluorescence images of a frozen hydrated cell using hard X-ray nanoprobe. (A) Typical online view in reflection mode using the dedicated optical video microscope of the ESRF ID16A beamline. After manual blotting, a total ice thickness of about 5−10 µm was achieved that allows a clear view of the frozen hydrated cells. A region with Newton rings indicative of even much thinner ice is noticeable. (B) Representative cryo-X-ray fluorescence cellular distributions of physiological elements potassium (K), sulfur (S), and zinc (Zn). Please click here to view a larger version of this figure.
Figure 8: X-ray fluorescence images of a freeze-dried neuronal cell using hard X-ray nanoprobe. (A) Typical bright field microscopy view of resultant freeze-dried primary cortical neuronal cells directly cultured onto the Si3N4 membrane. Scale bar = 200 µm (B) Representative room temperature X-ray fluorescence images of a single freeze-dried hippocampal neuron showing the distributions of physiological elements potassium (K), sulfur (S), and zinc (Zn). Scale bar = 2 µm. Please click here to view a larger version of this figure.
Cryo-electron microscopy (cryo-EM) won the 2017 Nobel Prize in chemistry and as such the development made by J. Dubochet on vitrification of biological material for the high-resolution structure determination of biomolecules in solution25. As reported by Dubochet in his Nobel lecture “Knowing how to vitrify a droplet of water is one thing, preparing a biological sample for biological observation is another”25. Cryopreparation steps are now considered the standard technique to mitigate radiation dose damage and study cells close to their native state. The preparation remains tedious, however. This is because electron microscopy, due to its unsurpassed spatial resolution, is sensitive to any ultrastructural artifact that occurs during the sample preparation. The synchrotron cryonanoprobes are now approaching similar difficulties going down to spatial resolutions as low as 13 nm in the high energy X-ray range26. Hard X-ray microscopy can analyze entire cells while electron microscopy suffers from the poor penetration depth of electrons enabling only very thin cell slices to be observed.
Monolayers of cells are thin enough so that by plunge-freezing in liquid ethane, the required cooling rates for water vitrification are attained. In theory, cooling rates as high as 108 K/s are possible using high-pressure freezing27 which allows vitrification of specimens too thick for plunge freezing. A cooling rate of 105 K/s, required to allow full vitrification of the sample at ambient pressure28, is reached reproducibly using the automatic plunge-freezing machine and parameters presented here. This allows a researcher to vitrify thin biological specimens (<10 µm) such as a monolayer of cells12,13,14,15,29,30 by plunge-freezing in liquid ethane.
An important challenge with this protocol is to also preserve as much as possible the chemical integrity of the intracellular content to provide reliable elemental distributions within the cell in 2D or 3D. As published elsewhere2,16,17,31, in the case of elemental imaging at the subcellular level, the analysis of frozen hydrated cells should be considered. Otherwise, the combination of plunge-freezing and freeze-drying of cells can be used for room temperature analysis. For the latter, the amorphous ice is removed through the process of sublimation, while the bound water molecules are removed through the process of desorption. This process may be far from ideal compared to frozen hydrated samples due to the possible alteration of the cellular membranes and the morphology of some subcellular structures32. Also, for speciation studies, the water extraction may lead to metal speciation artifacts. Still, it has been successful and the best alternative to frozen hydrated samples for elemental imaging at sub-100 nm levels2,16,17,18,20,33,34,35,36.
As it has been reported37, the quality of cryopreserved cellular preparations can be evaluated through the potassium-to-sodium K/Na ratio. Unfortunately, it cannot yet be determined with the hard X-ray nanoprobe used here, due to the low energy cut-off of the silicon drift detector used to detect the X-ray fluorescence photons of the elements (E ≥ 1.3 keV magnesium). Indeed, a high K/Na ratio (>10) that can be measured using TOF-SIMS, EPMA, or nuclear microprobe PIXE16,37 is indicative of the preserved chemical integrity of the cell compared to the expected K/Na of 25 in a living cell37. This can be supported by a concomitant low Cl/K ratio38. Still, imperfect vitrification, particularly if the speed of sample cooling is too low, can lead to the formation of large ice crystals that can damage cell membranes and organelles, consequently altering the distribution of chemical elements. Although there is no routine procedure to monitor this potential damage and impact on the intracellular distribution, the above elemental ratios and the possibility to image the cell at high resolution using X-ray phase contrast or cryo-soft X-ray microscopy can be the best approaches to support good preservation of intracellular compartments with concomitant preservation of the elemental integrity. The combination of these techniques and the use of newly developed cryocorrelative fluorescence optical microscopes will help assess to what extent this damage occurs and affects the intracellular elemental distribution.
Overall, a detailed and comprehensive protocol to prepare cellular samples for synchrotron X-ray fluorescence nano-analysis is presented. It is a good starting point for the research community, helping to solve the difficult issue of how to prepare appropriate cellular samples for 2D and 3D elemental imaging at (cryo) hard X-ray nanoprobes. These approaches can be merged with optical fluorescence and electron microscopy capabilities for in-depth correlative chemical and structural imaging of cells.
The authors have nothing to disclose.
The experiments on the nano-imaging beamline ID16A were performed in the frame of ESRF proposals LS2430, LS2303, and LS2765.
Ammonium Acetate solution, BioUltra, for molecular biology, ~5M in H2O | SIGMA | 09691-250mL | One can prepare the required solution from high-grade ammonium acetate powder and ultrapure water, pH and osmolarity needs to be adjusted anyway. |
B27 supplement, 50x | Life Technologies, Invitrogen | 17504-044 | for hippocampal neuron culture |
Dulbecco’s Phosphate Buffered Saline, DPBS, ([-] CaCl2, [-] MgCl2) | GIBCO | 14190-094 | cell culture |
DMEM with Phenol Red/Glutamax I (Medium ATCC modification) | GIBCO | 21885025 | cell culture |
Dulbecco’s modified Eagle medium (DMEM) | Life Technologies, Invitrogen | 31966-02 | for hippocampal neuron culture |
Dumont Tweezers #5, Straight Self-closing, 0.05×0.01mm Tips, Biology | World Precision Instrument | 501202 | |
Emitech K750X Peltier-Cooled EM Freeze Dryer | Quorum Technology | EK3147 | |
Ethane N45 | Air Liquid | p0505s05r0a001 | C2H6 > 99,995 % |
Fetal Bovine Serum, Performance Plus, certified One Shot format, US origin | GIBCO | A31604-02 | cell culture |
HBSS 10x | Life Technologies, Invitrogen | 14185-052 | for hippocampal neuron culture |
Leica GP quick-release forceps | Leica | 16706435 | |
MDA-MB-231 cell line, an epithelial, human adenocarcinoma breast cancer cell | ATCC | ATCC HTB-26 | cell culture |
Neurobasal medium | Life Technologies, Invitrogen | 21103-049 | for hippocampal neuron culture |
Nunc 4-Well Plate | Thermo Fisher | 176740 | cell culture |
Osmo1 Single-Sample Micro-Osmometer | Advanced Instruments | Osmo1 | Alternative can be found at Fisher scientific (Wescor Inc. VAPRO® Vapor Pressure Osmometer) |
Penicillin-Streptomycin | SIGMA | P4333 | cell culture |
poly-L-lysine | SIGMA | P4707 | Other type of coating can be used that is dependent of the cell type to be cultured on the membrane, other adhesion factors such as fibronectin, collagen, polyornithine can be tested accordingly. Cell can be cultured directly on silicon nitride membrane, but the latter are slightly hydrophobic and adhesion factors are recommended unless the membrane are processed to be hydrophilic (glow plasma discharged). |
Plunge freezing robot Leica EM GP main unit | Leica | 16706401 | Alternative for automated plunger are the Vitrobot Mark IV (FEI), CryoPlunge 3 (Gatan), MS-002 Rapid Immersion Freezer (EMS). Manual home-made system can be used but an environment-controlled chamber is an asset for plunge-freezing. |
Silicon nitride membrane (Si3N4) | Silson Ltd. | SiRN-5.0(o)-200-1.5-500-NoHCl | The proposed silicon nitride membrane type is optimised for analysis at ID16A ESRF X-ray nanoprobe, The 500 nm thickness of the membrane was chosen being more robust for cellular manipulation and cryofixation detailed within this protocol. Membrane with thickness of 200 nm or below can also be used although quite fragile, and other design of silicon nitride membrane can be purchased (for example TEM compatible membrane…) from Sislon or other company such as Norcada, SPI supplies, Ted Pella, EMS, LabTech, Neyco… |
Trypan blue solution 0.4% | GIBCO | 15250061 | cell culture |
Trypsin-EDTA, 0.05% | GIBCO | 25300-054 | cell culture |
Ultratrace Elemental Analysis Grade, Ultrapure Water | Fisher Chemicals | W9-1 | MilliQ water can be used but has to be tested for trace element level of contamination using for example ICP-MS analysis. |
Whatman No. 1 filter paper with precut hole | Leica | 16706440 | Alternative filter paper may be used and must have an outer diameter of 55 mm, the Punch for filter paper system from Leica (ref.16706443) can be used. |