In Situ Detection and Single Cell Quantification of Metal Oxide Nanoparticles Using Nuclear Microprobe Analysis

1. Sample Holder Preparation

1. Sample holder design and preparation
   1. Manufacture a sample holder by drilling a 5 mm x 5 mm square in a 1-mm thick PEEK frame.
   2. Clean by rinsing with ethanol 70% (v/v) and keep in sterile plates until ready to use.
      Note. A sample holder appropriate for cell culture and cell handling is required. It needs to be designed for cell culturing, in vitro observations with optical microscopy, and nuclear microprobe analysis and imaging. This holder is made of a PEEK frame¹³.
2. Sample holder preparation
   1. Prepare the Formvar solution by dissolving 1 mg of Formvar powder in 100 mL of chloroform.
   2. Stretch the polycarbonate foil on a metallic frame so that it presents no fold.
   3. Use a sterile tip to spread the Formvar solution around the sample holder hole.
   4. Put down delicately the sample holder with glue onto the stretched polycarbonate foil (a 5 mm x 5 mm square).
   5. Repeat the previous sequence to prepare one sample holder for each replicate.
      Note. The polycarbonate (PC) film is biocompatible, thick enough and resistant to the different protocols and analytical constraints.
      Caution– Chloroform is toxic. Avoid inhalation, ingestion or contact with skin. Always use a properly functioning chemical fume hood and appropriate filters.
3. Sample holder sterilization
   1. Place the mounted sample holder in a conical flask with 50 mL of ethanol 70% (v/v) under agitation at 180 rpm and +37 °C overnight, using an incubator/agitator.
   2. Rinse the holder several times in sterile distilled water.
   3. Air dry them in sterile conditions and expose them to ultraviolet light (germicidal lamp from Biosafety bench, class II) for 30 min on each side.
   4. Keep the samples in sterile 12-well plates (one sample holder per well) until ready to use.
      Note: Multiple sample holders can be stored at room temperature in sterile and dry 12-well plates sealed with parafilm for several days.

2. Growth of Cells in the Appropriate Sample Holder.

Caution: Protocol must be carried out in a biosafety laminar flow bench (Class II) to exclude contaminating micro-organisms. Handle antibiotics (e.g. penicillin, streptomycin) with gloves. Respect best practices when handling biological materials (Cell lines, genetically modified derived human cells).

Critical: The cell lines used should be checked to ensure that they are not infected with Mycoplasma.

1. Transfect U2OS cell line with plasmid bearing Matrix-roGFP ^17,18,19 using a transfection method in accordance to protocol established by manufacturer.
2. To confirm transfection with the plasmid-carrying the biosensor and to prevent plasmid loss, select and maintain the transfected cells on the appropriate culture medium.
3. Visualize transfected cells by fluorescence microscopy to ensure the transfection has occurred and to confirm the expression of the fluorescence and the display of a reticular and tubular mitochondrial network¹⁹.
   Pause point: Cells can be frozen in liquid nitrogen for several years.
4. Use the transfected cell population by culturing the cells in an appropriate medium in order to obtain sub-confluent cell populations. Grow cells at 37 °C, 5% (v/v) CO₂ in a saturated water atmosphere.
5. Seed cells in a concentration, such as they are at 80% confluence the day of fixation. Typically, a concentration of 500 cells per µL could be used. Harvest cells using 400 µL of Trypsin-EDTA 0.25% (v/v) and keep for 3 min at 37 °C. Stop trypsin action with 1 mL of culture medium. Pellet the cells by centrifugation for 5 min at 230 x g and +4 °C, then remove supernatant, and add the desired volume of fresh culture medium.
   Note.The protocol is applicable for all cellular types and the number of cells seeded is dependent on the cell size and on cell doubling time.
   Caution: Avoid subjecting trypsin, antibiotics, and serum to repeated freeze-thaw cycles. Keep them sterile. Divide the stock solution into aliquots and freeze them at −20 °C. Store the aliquots until the expiration date. Carefully rinse the cell pellet in order to completely remove the trypsin. Traces of residual trypsin will delay and decrease the plating efficiency.
6. Count the cells and perform a dilution with fresh complete culture medium kept at 37 °C in order to obtain a cell suspension with 500 cells per µL.
   Note: The concentration of the cell suspension has to be adapted as a function of the cell type, in order to plate a 40 µL drop.
7. Plate a 40 µL drop onto the center of the polycarbonate foil. Carefully place the sample for 2 h at +37 °C, 5% (v/v) CO₂ in a saturated water atmosphere.
   Critical: Once the sample is placed in the incubator, limit as much as possible any mechanical movement to favor fast cell attachment. According to the cell type, it could be necessary to incubate cells longer than 2 h for optimal platting efficiency. Check that the incubator atmosphere is well saturated to prevent drops from evaporating.
8. Check that cells are well-attached on the polycarbonate foil using an optical microscope. Gently add 2 mL of fresh complete medium and keep for 24 h.

3. Nanoparticles Preparation and Exposure

NOTE: Fluorescent dye-modified TiO₂ NPs were designed, synthesized, and chemically modified with tetramethyl rhodamine isothiocyanate (TRITC).^20,21 This surface modification allows nanoparticle detection, tracking and localization in situ and in cellulo in both living and fixed cells or in multicellular organisms.^12,13,18

Caution: Nanomaterials and Nanoparticles must be handled with care. Avoid inhalation, ingestion or contact with skin. To prevent dissemination in air, nanoparticles are maintained in solution (ultrapure water).

1. Prepare a suspension of 1 mg.mL⁻¹ of^TiO₂ NPs in ultrapure water. Disperse the TiO₂ NPs using intense 1-min sonication pulses at RT (750 W, 20 kHz, amplitude: 30%) using an ultra-sound generator and a dedicated conical microprobe.
2. Dilute TiO₂ NPs at the desired concentration in the culture medium in order to obtain an exposure suspension of 4 µg.cm⁻² (final concentration). Replace medium with the appropriate volume of medium containing NPs on cells and mix gently for homogeneous distribution of the TiO₂ NPs. Prepare control cells similarly without the addition of TiO₂ NPs.
3. Incubate the cell populations for 24 h at 37 °C, 5% (v/v) CO₂ and a saturated water atmosphere.

4. Paraformaldehyde fixation and fluorescence microscopy.

1. Prepare a fresh solution of paraformaldehyde solution (PFA, 4% w/v) buffered in Phosphate Buffer Saline (PBS, pH 7.4).
   1. Dissolve 4 g of PFA powder in 100 mL of PBS. Heat the solution to 65 °C while stirring using a magnet and a magnetic stirrer in a fume hood. Increase the pH by adding 1 M NaOH one drop at a time until the solution clears. Cool the solution to room temperature and adjust the pH to 7.4. Use the freshly prepared solution immediately or keep at +4 °C and protect from light.
      Note: Pre-made PFA solutions could be used however an extemporaneous preparation of PFA guarantees better fixation quality and long-term conservation of the fixed samples.
      Caution: PFA is toxic; avoid inhalation, ingestion or contact with skin. Always use a properly functioning chemical fume hood and appropriate filters.
2. Once, the incubation time has elapsed, remove the cell culture medium containing the TiO₂ NPs. Rinse the cell populations once with fresh culture medium and once with PBS (2 mL). Remove PBS, rinse quickly with an aliquot of fresh and cold PFA (4% w/v, +4 °C).
   1. Add PFA (2 mL, 4% w/v, +4 °C). Incubate 15 min at room temperature.
   2. Remove the PFA, rinse the cells with PBS (2 mL, 3 times, 5 min) under agitation.
      Pause point: These chemically fixed samples can be used for the "plunge-freeze" procedure after fluorescence imaging (go to step 5) or used only for fluorescence imaging (go to step 4.3).
3. Stain the nucleus with Hoechst³³³⁴² incubating the cells for 10 min in PBS. Hoescht³³³⁴² is used at a final concentration of 500 nM. After incubation remove the solution and rinse with PBS.
   Caution: Hoechst³³³⁴² is cell permeant and may be toxic. Avoid direct contact, and use gloves while preparing and using Hoechst³³³⁴².
   Critical: Ensure that the Hoechst³³³⁴² staining solution is freshly prepared and maintained in sterile conditions.
4. Process fixed samples for in situ and single cell imaging using fluorescence microscopy (Figure 1).

5. "Plunge-Freezing" Fixation and Dehydration

1. Prepare an aluminum transfer plate by cooling it in liquid nitrogen. Store the plate into a box filled with liquid nitrogen and maintain the plate surface above the liquid in the cold nitrogen vapor.
   Note: The transfer plate can be made of any metallic plate (here, we used aluminum) that could be cooled down to liquid nitrogen temperature, and that can enter the freeze-dryer sample chamber.
   Critical: The box should be kept closed as much as possible in order to prevent water vapor deposition onto the cold plate surface. The sample stored on the plate during preparation should not be covered by liquid nitrogen.
2. Rinse cells once in culture medium and then twice more, briefly, in sterile and ultrapure water to get rid of any trace of remaining extracellular salts.
   Critical: Ensure that the media are freshly prepared and maintained in sterile conditions. Heat all the media at 37 °C before being used. The rinse must be very brief (few seconds) and the excess of liquid on the samples removed as fast as possible.
3. Plunge-freeze the cells at -150 °C in liquid nitrogen-chilled 2-methylbutane during 30 s and place them onto the aluminum transfer plate. Store samples here during the preparation of all other samples. When samples are all cryofixed, transfer all-at-once by placing the transfer plate in a freeze-dryer.
   Critical: The overall cryofixation process should not last more than 20 min in order to prevent structural modifications to appear in samples temporarily stored in the transfer box.
4. Freeze-dry the samples using the following sequences: 1) perform a primary desiccation for 12 to 24 h (-99 °C, 10^-3 mbar) at low pressure and low temperature, then 2) perform a secondary desiccation phase for at least 24 h, increasing the plate temperature to +40 °C while keeping the pressure low (+40 °C, 10^-3 mbar).
   Caution: Liquid nitrogen is extremely cold and can cause severe frostbite or eye damage upon contact. Use adapted bench top containers for transport and wear safety equipment (cryogenic gloves, eye and face protection).
   Caution: 2-Methylbutane is extremely flammable. A harmful contamination of the air can be reached rather quickly on evaporation of this substance at +20 °C. Avoid inhalation, ingestion or contact with skin. Use breathing and eye protection, and protective gloves. Always use a properly functioning chemical fume hood. May be stored at +4 °C.
   Critical: Use an appropriate thermometer (-150 °C) to monitor the 2-Methylbutane temperatures during the "Plunge-freeze" session. The 2-methylbutane must be kept cool in a liquid phase. Transferring cryofixed samples to the ambient atmosphere may cause cellular damage due to the temperature increase or water vapor condensing on the sample surface. Accordingly, the transfer should be made as fast as reasonably possible (30 s)
   Pause point: After cryofixation, samples can be stored at room temperature for several days in sterile and dry conditions (protected from dust and moisture). Carefully handle the samples with fine forceps and place them in a sterile 12-well plate sealed with parafilm. Desiccant can be used to dry the atmosphere.

6. Nuclear Microprobe Analysis

NOTE: Nuclear Microprobe Analysis was carried out at the microbeam line of AIFIRA (Applications Interdisciplinaires des Faisceaux d'Ions en Région Aquitaine) using the complementary ion beam analytical techniques Particle Induced X-ray Emission (µ-PIXE) and Scanning Transmission Ion Microscopy (µ-STIM). The facility is based on a 3.5 MV particle accelerator delivering light ion beams in the MeV energy range.^22,23

Pause point: AIFIRA is an ion beam facility hosted by the University of Bordeaux that offers an access to national and international teams after scientific evaluation of the proposed experiment.

1. Mount the PEEK sample holders on an apertured plate using double-sided tape.
2. Place the plate supporting sample in a vertical plane perpendicular to beam direction.
3. Close the analysis chamber and vacuum the analysis chamber.
4. Scanning Transmission Ion Microscopy (µ-STIM)
   NOTE: STIM is used to record areal density maps of cells after conversion of energy loss to cellular mass, taking advantage of the fact that the energy loss is proportional to the sample areal density (expressed in µg.cm^-2).
   1. Use a 2 MeV Helium (He⁺) microbeam as a probe with a size in the focal plane of around 300 nm in diameter and at low fluency (2000 ions.s^-1). Measure the energy of the transmitted ions with a planar silicon detector (PIPS detector, 25 mm², 11 keV energy resolution @ 5.4 MeV), placed behind the sample in the beam axis.
5. Particle induced X-ray Emission (µ-PIXE) and Rutherford Backscattering Spectrometry (µ-RBS).
   NOTE: µ-Pixe and µ-RBS analyses provide the spatial distribution and quantification of chemical elements with a sub-micrometer resolution.
   1. Use a 1.5 MeV proton (H⁺) microbeam (50-150 pA), focused down to a diameter of 1 µm and scan over the same cells of interest spotted by STIM from 4 to 8 hours and around 100 x 100 µm².
   2. Collect induced X-ray photons emitted from atoms present in the sample (heavier than Na) by a high-resolution Si(Li) solid-state detector (145 eV energy resolution, @Mn-Kα) positioned at 45° from incoming beam axis. Use the detected photon energy to identify the nature of emitters (e.g. Z of element) and X-ray intensity to determine the element concentration.
   3. Simultaneously collect back-scattered protons at -135° with a silicon detector (partially depleted detector, 25 mm², 11 keV FWHM @ 5.4 MeV) to measure the total number of incoming particles and to normalize X-ray intensities.
      Critical: A collection of certified calibration standards for atomic concentration quantification is used in order to calibrate the X-ray detector response. Reference materials are a collection of thin atomic films deposited on 6.3 µm thick Mylar foils. Emitted X-Ray energies range from 0.6 (Li, K line) to 20.2 keV (Rh, K line).

7. Data analysis

1. Reconstruct chemical elemental maps using the IBA-J plugin for ImageJ.²⁴
   NOTE: Dedicated software in the form of a plugin for ImageJ has been developed to process raw nuclear microprobe analysis data. Raw data correspond to a list of events arising from particle beam interaction with cells that are recorded along with the beam position as a chronological sequence.
   1. Use the IBA-J plugin to sort events according to their type: transmitted ion energy (STIM), backscattered ion energy (RBS) or X-ray photon energy (PIXE). Then, process separately each type of data.
   2. Calculate STIM area density map
   3. Calculate average X-ray photon energy spectra and define for each chemical element of interest an energy window in order to retrieve the element spatial distribution.
   4. Define regions of interest (ROI) (e.g. individual cells, dense structure, aggregates, etc.) and calculate the corresponding x-ray spectra.
2. Analyze the corresponding RBS spectra in order to calculate the total number of incident particles²⁵.
3. Fit X-ray spectra using the Gupix software²⁶ in order to determine the element concentration for each ROI.
   NOTE: Typical limit of detection (LOD) for the method is in the range 1 to 10 µg.g^-1 in dry mass depending on the atomic number of elements (LOD is decreasing with Z).