Human DLBCL cell lines and culture conditions
MD-901, OCI-LY19, and SU-DHL4 DLBCL cell lines were obtained from José Angel Martinez-Climent (Centro de Investigación Médica Aplicada, Pamplona, Spain). Cells were grown in RPMI-1640 GlutaMAX medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 100 U/mL penicillin, and 100 µg/mL streptomycin (Gibco) at 37°C with 5% CO2.
For glutamine or glucose deprivation experiments, DLBCL cells were grown in RPMI-1640 medium supplemented as above without either glutamine or glucose.
Antibodies and reagents
Metformin (PHR1084) and 2-deoxy-D-glucose (2-DG, D8375) were purchased from Merck (Darmstadt, Germany), and L-asparaginase (®Kidrolase) was a kind gift from Isabelle Madelaine-Chambrin and Nathalie Jourdan (Service de Pharmacie Centrale Hôpital Saint-Louis). The antibodies were purchased from Santa Cruz Biotechnology (p70 S6 kinase sc-8418; 4EBP1 sc-9977; p38alpha/beta MAPK sc-7972; ERK1/2 sc-514302; β-actin sc-47798; GAPDH sc-32233), Cell Signaling Technology (Phospho-p70 S6 kinase (Thr389) #9234; Phospho-4E-BP1 (Ser65) #9451; Phospho-p38 MAPK (Thr180/Tyr182) #4511; Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) #4370; 4EBP1 #9452), and Merck (β-actin, A5441).
Measurement of intracellular ATP content
Intracellular ATP content was measured using an ATP luminescence detection kit (CellTiter-Glo® Luminescent Cell Viability Assay, Promega, Madison, WI, USA) according to the manufacturer's instructions. Briefly, 4 x 105 cells were seeded in 100 µL of complete medium. Cells were treated for 1 h with or without 20 mM 2-deoxy-D-glucose (2-DG) at 37°C followed by 30 min at room temperature to inhibit glycolysis. At the end of the incubation time, 100 µL of CellTiter-Glo solution was added, and cells were incubated for 10 min at room temperature. The luminescence signal (relative luminescence units (RLU)) was recorded with a microplate reader (Centro LB 960 microplate luminometer, Berthold Technologies, Bad Wildbach, Germany). The difference between total ATP content and ATP produced under 2-DG treatment results in glycolytic ATP.
Apoptosis Assays
DLBCL cells were harvested and washed twice with cold PBS. Cells were resuspended in 1X binding buffer containing Annexin V/PE (BD Biosciences Pharmingen, San Diego, CA, USA) and 4’,6-diamidino-2-phenylindole (DAPI, Molecular Probes, Life Technologies, Carlsbad, CA, USA) for 15 min at room temperature. The samples were then subjected to cytometric analysis with a MACSQuant Analyzer 10 Flow Cytometer (Miltenyi Biotec, Bergisch Gladbach, Germany), and the data were analyzed using the Flowjo v10.2 software (Ashland, OR, USA).
Measurement of Mitochondrial Transmembrane Potential
For the determination of mitochondrial transmembrane potential (ΔΨm), cells were stained with 100 nM of tetramethylrhodamine, methyl ester (TMRM) (Molecular Probes, Life Technologies, Carlsbad, CA, USA) in RPMI-1640 GlutaMAX medium for 30 min at room temperature. Cells were evaluated by cytometric analysis as above.
Cell viability assay
Cell viability was assessed using trypan blue dye exclusion.
Immunoblotting
Immunoblots were performed as previously described21.
NMR-based metabolomics
Exponentially growing DLBCL cells were seeded at a density of 2x105-2,5x105/ml in a total volume of 25 ml in 75 cm2 flasks at the time of treatment with antimetabolic drugs (total 5x106 cells/condition) and harvested 24 h later. Decaplicates of either extracellular medium or dry cell pellet samples were prepared for each condition: Extracellular media were added to the deuterated buffer with 3.57 mM of trimethylsilylpropanoic acid (TSP) concentration to obtain a final concentration of 1 mM of the TSP sample in the NMR tube, following standard protocols22. Dry cell pellets were treated with 400 µL of ice-cold methanol and 65 µL of ice-cold water. A volume of 200 µL of ice-cold chloroform, then 200 µL of ice-cold water and finally 200 µL of ice-cold chloroform were further added. The samples were then left on ice for 15 min, and centrifugated at 2000 rpm for 15 min. The upper methanol/water phase (containing polar metabolites) and the lower chloroform phase (containing lipophilic compounds), were transferred into separate glass vials. Solvents were removed under a stream of nitrogen for 30 min. The water phases were put in the freeze dryer one night. The dry water phase samples were resuspended in 580 µL of NMR buffer (100 mM sodium phosphate buffer pH 7.4, in D2O, with 3.57 mM TSP and 6 mM NaN3) to obtain the polar phase extract. The lipophilic phases were resuspended in 600 µL of deuterated NMR solvent (2:1 mixture of pure CDCl3 and CDCl3 containing 0.03% of TMS, to obtain a final solution of 0.01% of TMS) and then vortexed. After centrifugation (5 min), 580 µL of the supernatant was directly transferred into an NMR tube to prepare the organic phase extract.
All samples were measured on a 500 MHz Bruker Avance III spectrometer equipped with a SampleXpress automation sample changer and a cryogenic 5 mm 13C/1H dual probe with Z-gradient. The exometabolome sample spectra were acquired using a classical 1D 1H experiment used for the metabolomics analysis of biofluids by NMR (1D-NOESY pulse sequence with presaturation for water suppression). The endometabolome samples were acquired using the classical experiment used for the metabolomic analysis of tissue extracts by NMR (1D-CPMG pulse sequence with presaturation for water suppression)22. The operating software was TopSpin 3.1 1 (Bruker BioSpin, France).
Metabolite Identification. For each NMR spectrum, the standard processing protocol was applied, including Fourier transform, phase correction, baseline correction, and calibration. Spectra were aligned to a reference signal using TSP as a chemical shift standard (0.016 ppm). For metabolite identification, 1H NMR spectra were analyzed using Chenomx NMR Suite 8.0 (Chenomx Inc.). Metabolite identification was performed using the spectral reference library and fitting peak intensity and location to the observed signals.
Statistical Analysis. The processing of raw data was carried out using NMRProcflow, including baseline correction, chemical shift calibration, data alignment, and variable-sized bucketing23. For all datasets, a threshold corresponding to a signal-to-noise ratio of 3 was applied. For normalization, we chose to calculate for each sample the intensity variation between the spectrum of this sample and the reference spectrum recorded on the growing medium (RPMI-1640 left under the same experimental conditions as the sample). In the second step, we normalized this intensity variation with the integration of the number of cells over the duration of the treatment. Subsequently, we used SIMCA 15 software (Umetrics) to perform principal component analysis (PCA) or orthogonal projections to latent structure discriminant analysis (OPLSDA) in order to discriminate cancer cell line classes. Pareto scaling was used in both analyses. MetaboAnalyst 6.024 was used to perform t-tests and determine p-values with FDR correction and to generate box plots (https://www.metaboanalyst.ca/).
Antimetabolic therapy
Three patients followed at the Hôpital Saint-Louis, with a confirmed diagnosis of R/R DLBCL, were treated after consent with an optimized antimetabolic drug combination, including the sequential administration of L-asparaginase and metformin followed by temsirolimus, based on our previous work and our novel preclinical data included in the present study25. This combination was discussed and approved on June 26, 2018, by the scientific committee of the Lymphoma Study Association (LYSA). Treatment consisted of L-asparaginase (K, ®Kidrolase, Jazz Pharmaceuticals, 10 000 UI/m2) over 60 min on days 1, 3, 5, 7, 9, 11, and 13, metformin (M, Mylan, 1000 mg/day) once a day continuously from day 1 to day 14, and temsirolimus (T, ® Torisel, Pfizer, 75 mg/week) administered on day 1 of week 3 and week 4. Response assessment was scheduled at month 1 and month 3 based on Lugano criteria26.
Tissue processing and hematoxylin and eosin staining of DLBCL patient biopsies
Core biopsies obtained from patients with DLBCL were fixed in buffered formalin for 24 h and then transferred to 70% ethanol for 6 h. Subsequently, tissues were dehydrated using increasing concentrations of ethanol (70%, 95%, 100%) in an automated processor (Logos One, Microm France), followed by a final incubation in isopropanol. After dehydration, tissues were impregnated with paraffin and embedded using a tissue embedding system (Tissue tek), followed by sectioning on a microtome (Autosection, Sakura) with a thickness of 4µm. Slides were stained with hematoxylin and eosin at the department of Anatomic Pathology at Hospital Saint Louis, Paris, France, following standard protocols.
Statistics
Statistical significance was assessed using unpaired t-test (Prism 8.0, GraphPad Software, San Diego, CA, USA). A p-value of < 0.05 was considered statistically significant, with the following degrees: * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001.