Paravision software

In Fig. 5b, c, the reaction buffer (5 units/mL hSHMT1, 50 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM EDTA, 1 mM DTT, 20% D₂O, 0.1% DMSO, with or without 10 µM SHIN1) was preincubated at 37 °C for 1 h. ¹⁹F NMR probe 2 was added to the solution and incubated at 37 °C. The ¹⁹F NMR spectra were measured at 37 °C (24 scans). Trifluoroacetic acid (–76.5 ppm), a counter anion of the probe, was used as the internal standard for ¹⁹F NMR. In Fig. 5d, ¹⁹F NMR probe 2 (final conc. 1 mM) was added to the rat liver homogenate (2.42 mg proteins/mL in PBS), incubated at 37 °C, and then subjected to ¹⁹F NMR analysis.
In Fig. 5e, the enzymatic reaction solution (500 µL) containing 10 mM of probe and hSHMT1 with or without 10 µM inhibitor (±)-SHIN1 was incubated at 37 °C. After 1 day, the reaction was stopped by adding 0.5 µL of 10 mM (±)-SHIN1. MR images were recorded on a BioSpec 117/11 system and processed by using ParaVision software (Bruker Biospin). The 200 µL reaction samples were dispensed into PCR tubes. The rapid acquisition with refocused echoes (RARE) method was used for ¹H and ¹⁹F imaging. For ¹⁹F imaging, the acquisition matrix size was 64 × 32 (zero filled to 128 × 64 for image processing) with a field of view of 8.0 × 4.0 cm. The repetition time was 1000 ms, and the effective echo time was 48.0 ms. The number of accumulations was 128.

Mice bearing BCBM were imaged using MRI 2 weeks following intracranial injection of BCBM organoids. This corresponds to the initiation of the saline or doxorubicin treatment in vivo. MRI was performed with a 7-T BioSpec 70/20 USR (Bruker, Billerica, MA USA). T1-weighted postcontrast sequence with a 3-ms echo time, 235-ms repetition time, and a flip angle of 30° was used. Gadoterate meglumine (Dotarem; 0.025 mmol/ml; Guerbet, Villepinte, France) was used as a contrast agent and was injected intravenously through a cannula inserted into the tail vein. Mice were sedated with 2% (v/v) isoflurane before and during imaging, and their heart rate and frequency were monitored throughout the procedure. Image acquisition and processing were performed with Paravision software (v6.0.1; Bruker).

For MPI reconstruction of the different particle types, the multi-contrast MPI approach was used [22 (link)], i.e., combining both system matrices, the KLB system matrix and the Bayoxide E8706 system matrix, in one system of equations. Image reconstruction was performed with a reconstruction framework developed in-house. To combine the two patches, a joint reconstruction was used [25 (link)]. The linear system of equations was set up using a Tikhonov regularization and solved using the Kaczmarz algorithm [26 (link)] using 3 iterations and a relative regularization parameter of 0.05. For the measurements, a subtraction with an empty measurement was performed to increase signal quality. For the reconstruction, frequency components between 75 kHz and 625 kHz with a signal-to-noise ratio larger than 3 were selected.
The reconstruction of the MRI data was performed with Paravision software (Bruker BioSpin, Ettlingen, Germany).