Supplemental Information: Material and Methods. Human subjects The study was approved by the ethics committee of the University Hospital of ErlangenNuremberg (approval number: 3779). Samples of AML patients and healthy donors (HD) were collected upon patient’s informed consent and in accordance to the Declaration of Helsinki. Peripheral blood mononuclear cells (PBMCs) and bone marrow cells (BMCs) from a total of 25 AML patients were collected. Patients’ characteristics are detailed in supplemental Table 1. Mesenchymal stromal cells (MSCs) were isolated from iliac crest bone marrow aspirates from six healthy donors (approval number: 200_12) and expanded while fulfilling uniformly minimal MSC criteria. Cell lines The AML cell lines KG-1, OCI-AML3, and THP-1 were obtained from DSMZ (Braunschweig, Germany) and the human BM-derived stromal cell line HS-5 from ATTC (Manassas, VA, USA). Cell isolation PBMCs and BMCs were isolated from peripheral blood and bone marrow blood respectively using Ficoll-Paque (GE Healthcare, Piscataway Township, NJ, USA). Primary CD33+CD34+ AML cells were further purified from PBMCs or BMCs using fluorescence activated cell sorting (FACS Astrios, Beckman Coulter, Brea, CA, USA). Co-culture experiments Cells were cultured in 24-well plates (Corning Inc., Corning, NY, USA) in RPMI 1640 medium (Life Technologies, Carlsbad, CA, USA) supplemented with 10% fetal calf serum (PAN Biotech, Aidenbach, Germany), 1% L-glutamine (Life Technologies, Carlsbad, CA, USA), and 0,4% penicillin-streptomycin (Sigma-Aldrich, St- Louis, MO, USA) under standard conditions (37°C, 5% CO2). For co-culture experiments HS-5 cells or MSCs were 1 seeded 24 hours prior the addition of AML cells in a HS-5/MSC to AML cell ratio of 1:10. Co-cultures were performed for 24-72 hours. Specific cell death The cell viability was assessed utilizing a Count & Viability Assay Kit for a Muse Cell Analyzer (Merck Millipore, Billerica, MA, USA) according to the manufacturer’s instructions or FACS-based with viable cells being defined as 7-AADneg/Annexin-Vneg. Proportion of specific cell death was calculated according to following formula: specific cell death (%) = 100 × (% dead cells − % baseline dead cells) / (100% − % baseline dead cells). Antibodies and flow cytometry (FACS) Cells were stained using fluorochrome-coupled antibodies (Supplemental Table 2). Labeling was performed in presence of an Fc receptor-blocking reagent (Biolegend, San Diego, CA, USA). Dead cells were excluded from further analysis using a LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (Life Technologies). Intracellular staining (ICS) was performed using BD Cytofix/CytopermTM reagents (BD Bioscience, Franklin Lakes, NJ, USA). For CXCL12 ICS cells were pre-treated with GolgiPlug (BD Bioscience). For intracellular detection of phosphorylated proteins CytofixTM and PhosflowTM Perm Buffer III (both BD Bioscience) were used. FACS data was acquired on an FACS Canto II cytometer (BD Bioscience) and analyzed by FlowJo version 9.5 software (Treestar, Ashland, OR, USA). Mitochondrial membrane potential The potentiometric dye JC-1 (Cayman Chemicals, Ann Arbor, MI, USA) was used to determine the electrochemical potential (ΔψM) across the mitochondrial membrane. Cells were stained for 30 min at 37°C followed by FACS analysis. Glucose and lactic acid measurement We determined the glucose and lactic acid concentration in cell culture supernatants using a Super GL Compact (Hitado, Möhnesee, Germany). 2 RNA preparation and quantitative real time PCR (qPCR) Total RNA was isolated from cell lysates (innuPREP, RNA Mini Kit, Analytic Jena, Jena, Germany) and transcribed to cDNA (Superscript First Strand Synthesis System, Life Technologies) via reverse transcriptase PCR using a Mastercycler Nexus (Eppendorf, Hamburg, Germany). The messenger RNA (mRNA) levels were quantified by qPCR (Quantitect SYBR Green PCR Kit, Qiagen, Hilden, Germany) on a Rotor Gene Q (Qiagen). The relative gene expression was calculated by normalizing the expression of the target gene to ß-actin using gene-specific primers. In selected experiments cDNA was subjected to a qPCR analysis of 84 genes involved in glycolysis (RT² Profiler™ PCR Array Glucose Metabolism, Qiagen) according to the company’s recommendations. Small interfering (si)RNA transfection The human BM stromal cell line HS-5 was transfected with CXCL12 siRNA purchased from Ambion (Life Technologies) at a concentration of 10 nM using Lipofectamine 3000 (Life Technologies). For determining the siRNA efficacy transfected and control cells and their supernatant were, at 48 hours post transfection, collected to measure CXCL12 mRNA and released CXCL12 protein respectively. Detection of CXCL12 Cell culture supernatants were analyzed by a sandwich enzyme-linked immunosorbent assay (ELISA) using monoclonal antibodies for human CXCL12 (Leinco Technologies, Inc., St. Louis, MO, USA). Reactive oxygen species (ROS) measurement Mitochondria-specific ROS were semi-quantified by FACS using MitoSOX (Life Technologies). Antioxidant capacity The cells’ antioxidant capacity was quantified in cell lysates using a colorimetric Antioxidant Assay Kit (Cayman Chemical) following the manufacturer’s instructions. 3 Glutathione levels Intracellular glutathione levels were semi-quantified by FACS using the ThiolTracker violet dye (Life Technologies). Glucose uptake Influx of glucose was semi-quantified by FACS based on the cells’ incorporation of fluorescently labeled glucose analogue 2-(N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino)-2Deoxyglucose (2-NBDG). Extracellular flux analyses The bioenergetic profile of AML cells was determined using an XF96e Extracellular Flux Analyzer (Seahorse Bioscience, North Billerica, MA, USA). Cells were seeded in specialized tissue culture plates at an optimized density of 1x105 cells/well using CELL-TAK (BD Biosciences). All measurements were carried out in octaplicates as described in detail previously. Glycolytic parameters were determined using the Glyco Stress Test (Seahorse Bioscience) that assesses changes of the extracellular acidification rate (ECAR/indicative for aerobic glycolysis) upon application of glucose (10 mM), oligomycin (1 µM), and 2-DG (100 mM). Responses of the cells’ oxygen consumption rate (OCR/indicative for oxidative phosphorylation) towards oligomycin (1 µM), FCCP (1.5 µM), and the combination of antimycin (3 µM) and rotenone (3 µM) were evaluated yielding basic mitochondrial parameters (Mito Stress Test, Seahorse Bioscience). The ECAR levels upon glucose injection reflect basal glycolysis. Blocking mitochondrial ATP production by oligomycin shifts the energy production away from mitochondrial oxidative phosphorylation (OXPHOS) towards aerobic glycolysis and thereby leads to an ECAR increase that reveals the cells’ maximal glycolytic capacity. The oxygen consumption rate (OCR), which acts as a surrogate for OXPHOS, was measured simultaneously. Oligomycin blocks complex V (F0F1-ATPase) that couples the electron transport chain with ATP synthesis. Relative OCR reduction following oligomycin treatment indicates the proportion of ATP production linked to respiration. 4 Reagents Dimethyl sulfoxide (DMSO), diclofenac sodium salt, and rapamycin were purchased from Sigma-Aldrich, AMD3100 from Merck Millipore, and Ara-C from the hospital pharmacy. Statistical analysis Comparisons for two groups were calculated using a paired or unpaired, two-tailed Student’s t-test. All statistical analyses were performed using GraphPad Prism Version 5 (GraphPad Prism Software Inc., San Diego, CA, USA). 5 Supplemental Table 1: Patients’ characteristics. UPN Sex Age, Years Cytogenetic Risk† BM Blasts, % 698 700 735 745 749 750 773 865 953 1007 1008 1016 1022 1036 1054 pAML2 872 905 838 1070 909 1103 739 1027 856 f f f f f m f m f m m f m m m m f m m m f m m m m 64 21 64 59 18 69 39 23 49 82 43 54 21 71 63 18 47 72 20 52 73 61 54 52 61 intermediate intermediate adverse favorable favorable favorable adverse favorable favorable favorable intermediate intermediate intermediate intermediate intermediate adverse intermediate adverse intermediate intermediate favorable favorable intermediate adverse intermediate 90 80 96 30 30 30 50 80 60 45 95 95 95 95 95 95 80 90 80 95 30 95 70 90 30 † Cytogenetic risk assessment based on Döhner H et al., Blood 2010 Abbreviations: UPN, unpersonalized patient number; m, male; f, female; BM, bone marrow 6 Supplemental Table 2: Antibody list. Antibody Fluorochrome Clone Isotype Company CD33 PE WM53 Mouse, IgG1, κ BioLegend CD33 CD34 APC BV421 WM53 561 Mouse, IgG1, κ BioLegend Mouse, IgG2a, κ BioLegend CD34 CD45 PE Cy7 V500 581 HI30 Mouse, IgG1, κ Mouse, IgG1, κ CD45 CD184 APC PE HI30 12G5 Mouse, IgG1, κ BioLegend Mouse, IgG2a, κ BioLegend CXCL12 GLUT-1 GLUT-2 GLUT-3 GLUT-4 pmTOR (pS2448) unconjugated APC PE FITC FITC PE 79018 202915 199017 polyclonal mAbcam48574 021-404 Mouse, IgG1 Mouse, IgG2B Mouse, IgG2A Rabbit, IgG Mouse, IgG2B Mouse, IgG1, κ Leinco Technologies R&D systems R&D systems Abcam Abcam BD Bioscience pS6 (pS235/pS236) p4EBP1 (pT36/pT45) 7-AAD Annexin-V PE PE PerCP Cy5.5 FITC N7-548 M31-16 Mouse, IgG1, κ Mouse, IgG1, κ BD Bioscience BD Bioscience BioLegend BioLegend 2-NBDG FITC BioLegend BD Bioscience Cayman Chemicals 7 Supplemental Table 3: The 25 most strongly upregulated gene transcripts of genes involved in the regulation of enzymatic pathways of glucose and glucose metabolism in AML cells upon stromal contact. Rank Gene Fold Change Name 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 PRPS2 SDHA PRPS1 SUCLG2 PGM3 SDHC PGM2 GBE1 ENO1 TPI1 ENO2 PGM1 G6PC3 FH GAPDH GALM SDHB PDK1 PC ACO1 ACLY PDPR HPRT1 ALDOC RPE 21,48 16,48 10,97 10,42 9,36 6,09 5,38 2,26 2,11 2,10 2,05 2,04 1,83 1,77 1,70 1,68 1,60 1,59 1,59 1,58 1,58 1,57 1,56 1,56 1,55 Phosphoribosyl pyrophosphate synthetase 2 Succinate dehydrogenase complex, subunit A, flavoprotein (Fp) Phosphoribosyl pyrophosphate synthetase 1 Succinate-CoA ligase, GDP-forming, beta subunit Phosphoglucomutase 3 Succinate dehydrogenase complex, subunit C Phosphoglucomutase 2 Glucan (1,4-alpha-), branching enzyme 1 Enolase 1, (alpha) Triosephosphate isomerase 1 Enolase 2 (gamma, neuronal) Phosphoglucomutase 1 Glucose 6 phosphatase, catalytic, 3 Fumarate hydratase Glyceraldehyde-3-phosphate dehydrogenase Galactose mutarotase (aldose 1-epimerase) Succinate dehydrogenase complex, subunit B, iron sulfur (Ip) Phosphoenolpyruvate carboxykinase 1 (soluble) Pyruvate carboxylase Aconitase 1, soluble ATP citrate lyase Pyruvate dehydrogenase phosphatase regulatory subunit Hypoxanthine phosphoribosyltransferase 1 Aldolase C, fructose-bisphosphate Ribulose-5-phosphate-3-epimerase 8 100 *** viability [%] 80 60 40 20 -H + SH 5 S5 0 CD33 Supplemental Figure 1: Primary CD33+CD34+ AML cells (n=16 patients) were cultured for 24 hours in presence/absence (+/-) of HS-5 cells and the AML cells’ viability assessed. The bars represent the standard error mean. Abbreviations: ***; p-value<0.001. CD34 gluco ECAR [mpH/min] 150 oligo 100 50 S5 H + H S5 0 + + H S5 80 S5 40 60 minutes + 20 100 0 0 0 200 H S5 0 50 KG-1 oligo + 50 100 gluco 300 H S5 100 oligo + 150 OCI-AML3 gluco 150 ECAR [mpH/min] 200 THP-1 + HS-5 - HS-5 H ECAR [mpH/min] 250 ECAR [mpH/min] gl uc os e ol ig om yc in 2D G Supplemental Figure 2: A representative dot plot analysis showing the FACS gating strategy for the sorting of peripheral blood- and bone marrow-derived CD33+CD34+ AML cells. Supplemental Figure 3: The extracellular acidification rate (ECAR), which is indicative for aerobic glycolysis was continuously measured in three human AML cell lines (THP-1, OCIAML3, and KG-1) following 24 hours of culture in presence or absence (+/-) of a human HS5 stromal cell line monolayer using an XFe96 flux analyzer. Alterations of ECAR in response to glucose (gluco) and oligomycin (oligo) application as exemplarily shown for THP-1 (left panel) yield basal glycolysis and glycolytic capacity. The reaction is abolished by 2-DG. Representative data for changes of basal glycolysis and glycolytic capacity upon stromal contact are shown for THP-1, OCI-AML3, and KG-1. The bars represent the standard error mean. 9 150 100 50 gl gl ECAR [mpH/min] 200 OCI-AML3 250 150 100 50 0 20 40 60 minutes 80 + MSC - MSC 200 150 100 50 0 0 uc os e ol ig om yc in 2D G uc os e ol ig om yc in 2D G uc os e ol ig om yc in 2D G gl KG-1 200 ECAR [mpH/min] ECAR [mpH/min] THP1 250 0 0 20 40 60 minutes 80 0 20 40 60 minutes 80 Supplemental Figure 4: Extracellular acidification rate (ECAR) as continuously monitored by an XFe96 flux analyzer is an indicator for aerobic glycolysis. Responses of ECAR towards glucose and oligomycin yield basal glycolysis and glycolytic capacity. Glycolysis is abolished by 2-deoxy-D-glucose (2-DG). AML cell lines (THP-1, KG-1, and OCI-AML3) were cultured in presence/absence of primary bone marrow-derived mesenchymal stromal cells (MSCs). In the follow, ECAR/aerobic glycolysis was assessed as displayed. The bars represent the standard error mean. % OCR upon oligomycin 80 pAML *** 60 40 20 100 *** 80 60 40 20 0 -H + SH 5 S5 0 -H + SH 5 S5 % OCR upon oligomycin cell lines Supplemental Figure 5: The oxygen consumption rate (OCR) as a surrogate for oxidative phosphorylation (OXPHOS) was assessed before (=baseline) and after oligomycin injection in AML cell lines (THP-1, OCI-AML3, and KG-1, n=9 experiments) and in primary CD33+CD34+ FACS-sorted AML cells (n=13 patients) cultured for 24 hours in presence/absence of HS-5 cells using an XFe96 flux analyzer. The extent of the oligomycinmediated OCR reduction (baseline OCR is set as 100%) correlates positively with the OXPHOS’s contribution to energy production. The bars represent the standard error mean. Abbreviations: ***; p-value<0.001. 10 OCR [pmol/min] 150 *** 100 50 -H + SH 5 S5 0 Supplemental Figure 6: The oxygen consumption rate (OCR) is a surrogate for the cells’ respiration/oxidative phosphorylation. OCR was measured using an XFe96 flux analyzer in AML cell lines (THP-1, OCI-AML3, and KG-1, n=9 experiments) previously cultured in presence/absence of HS-5 for 24 hours. The bars represent the standard error mean. Abbreviations: ***; p-value<0.001. 15000 JC-1 PE [MFI] MitoSOX [MFI] 3000 2000 1000 10000 5000 0 -H + SH 5 S5 -H + SH 5 S5 0 Supplemental Figure 7: Mitochondrial fitness was evaluated based on the mitochondrial production of reactive oxygen species (ROS) and the mitochondrial membrane potential of AML cell lines (THP-1, OCI-AML3, and KG-1, n=6-9 experiments) cultured in presence/absence of HS-5 cells for 24 hours. Both parameters were assessed by FACS using a probe specific for mitochondrial ROS (MitoSOX, Life Technologies) and a potentiometric dye (JC-1, Cayman Chemicals) respectively. Semi-quantification is based on the median fluorescence index (MFI). The bars represent the standard error mean. 11 cell lines 40 p<0.05 %al in/decrease [2-NBDG FITC MFI] %al in/decrease [MFI] cell lines 150 100 50 *** 30 20 10 0 G L G UT L 1 G UT L 2 G UT LU 3 T4 0 Supplemental Figure 8: AML cell lines (cell lines, n=9 experiments) were cultured for 24 hours in presence or absence of HS-5 cells. Expression of glucose transporters (GLUT1-4) was semi-quantified based on the according median fluorescence index (MFI) by FACS. Data is displayed as the %al GLUT1-4 MFI in-/decrease in response to stromal contact. Glucose uptake was semi-quantified in AML cell lines (cell lines, n=9 experiments) by FACS based on the MFI of the incorporated fluorescent glucose analog 2-NBDG. Data is displayed as the %al 2-NBDG MFI in-/decrease in response to stromal contact. The bars represent the standard error mean. Abbreviations: ***; p-value<0.001. 0.4 1000 0.1 0.0 O C KG 1 -H + SH 5 S5 0 0.2 I-A M L3 2000 0.3 P1 3000 - HS-5 + HS-5 TH * antioxidants [mM] Thioltracker [MFI] 4000 Supplemental Figure 9: AML cells lines (THP-1, OCI-AML3, and KG-1, n=9 experiments) were cultured in presence or absence of HS-5 cells for 24 hours. The total intracellular glutathione content was evaluated by FACS based on the median fluorescence index (MFI) of the Thioltracker probe (Life Technologies). Cells were also lysed and their antioxidant content was assessed using a fluorimetric assay (Cayman Chemicals). The bars represent the standard error mean. Abbreviations: *; p-value<0.05. 12 % specific cell death 80 - HS-5 + HS-5 60 40 20 0 0.1 1 10 100 Ara-C [µM] cell number Supplemental Figure 10: Primary AML cells (n=6) were cultured in presence or absence of HS-5 bone marrow stroma cells with increasing concentrations of Ara-C for 48 hours and specific cell death assessed using a FACS-based approach. UPN 1027 + HS-5 pmTOR + HS-5 pS6K1 + HS-5 p4EBP1 Supplemental Figure 11: Primary FACS-sorted CD33+CD34+ AML cells (pAML, n=5-9 patients) were cultured in presence/absence of HS-5 cells for 24 hours and afterwards analyzed by FACS in terms of pmTOR, pS6K1, and p4EBP1 as shown in representative histogram analysis. Abbreviations: UPN; unique patient number. 13 cell lines 1000 -H + SH 5 S5 0 1500 1000 500 0 3000 2000 1000 0 -H + SH 5 S5 2000 2000 p4EBP1 [MFI] ** -H + SH 5 S5 3000 4000 * pS6K1 [MFI] pmTOR [MFI] 2500 UPN 865 cell number cell number Supplemental Figure 12: The expression of phosphorylated/activated mTOR (pmTOR) and phosphorylated forms of its downstream molecules ribosomal protein S6 kinase 1/S6K1 and the eukaryotic initiation factor 4E binding protein 1/4 EBP1 (pS6K1 and p4EBP1) was evaluated by FACS based on the median fluorescence index (MFI). AML cell lines (THP-1, OCI-AML3, and KG-1, n=9 experiments) were cultured in presence/absence of HS-5 cells for 24 hours and afterwards analyzed by FACS in terms of pmTOR, pS6K1, and p4EBP1 MFI. The bars represent the standard error of the mean. Abbreviations: UPN; unique patient number, *; p-value<0.05, **; p-value<0.01. pmTOR UPN 749 BM PB pS6K1 Supplemental Figure 13: Primary PB- and bone marrow (BM)-derived FACS-sorted CD33+CD34+ AML cells from six individual patients were evaluated regarding their pmTOR and pS6K1 as shown in representative histogram analysis. Abbreviations: UPN; unique patient number. 14 B. 2000 1500 1000 250 + + + 0 HS-5 Rapa HS-5 Rapa + + + 3000 2000 1000 0 0 + + + HS-5 Rapa 50 + + + HS-5 Rapa + + + glycolysis basal capacity THP-1 untreated + HS-5 150 + HS-5 + RAPA 100 50 0 40 minute 60 80 100 50 0 O 20 500 0 200 0 * * ****** 100 2DG ol ig o gl uc os e D. HS-5 Rapa + + + 1000 500 0 0 HS-5 Rapa ECAR [mpH/min] 2000 4000 *** ** 1500 2-NBDG [MFI] 200 4000 * *** C KG I-A -1 M TH L 3 P O K -1 C G I-A -1 M TH L 3 P1 400 2500 % of stromal effect 600 * ** GLUT4 [MFI] GLUT2 [MFI] GLUT1 [MFI] 6000 GLUT3 [MFI] * * 800 C. lactic acid [mg/dl] A. Supplemental Figure 14: AML cells lines (THP-1, OCI-AML3, and KG-1, n=9 experiments) were cultured for 24 hours in presence or absence of HS-5 cells with/without simultaneous mTOR inhibition by rapamycin (100 nM). Next, we evaluated the effects of a concomitant mTOR inhibition on the AML cells’ expression of (A) glucose transporters (GLUT1-4), (B) glucose uptake (2-NBDG) as well as (C) lactic acid concentration in the cell culture supernatant. (D) AML cell lines from comparable, as indicated, experimental settings were used for glycolytic flux analyses (XFe96 flux analyzer). The extracellular acidification rate (ECAR), indicative for aerobic glycolysis, was measured continuously as displayed paradigmatically for THP-1 cells. Changes of ECAR upon addition of glucose and oligomycin (oligo) yield basal glycolysis and the cells’ glycolytic capacity respectively. Aerobic glycolysis is abolished by 2-DG. The impact of rapamycin on the stroma-mediated promotion of basal glycolysis and of glycolytic capacity is shown for THP-1, OCI-AML3, and KG-1 cells. ECAR levels measured for cells with stromal contact but without rapamycin treatment were set as 100%. The bars represent the standard error of the mean. Abbreviations: *; p-value<0.05, **; p-value<0.01, ***; p-value<0.001. 15 cell count HS-5 CXCL12 Supplemental Figure 15: The FACS analysis density plot displays the CXCL12 production in the human bone marrow stroma cell line HS-5. cell lines pAML 15000 10000 CXCR4 [MFI] CXCR4 [MFI] ** 10000 5000 * 8000 6000 4000 2000 0 + HS H 5 S5 -H + SH 5 S5 0 Supplemental Figure 16: Density of CXCR4 expression shown as the median fluorescence index (MFI) was assessed by FACS for AML cell lines (THP-1, OCI-AML3, and KG-1, n=9 experiments) and primary CD33+CD34+ AML cells (pAML, n=4 patients) cultured in presence/absence of HS-5 for 24 hours. The bars represent the standard error of the mean. Abbreviations: *; p-value<0.05, **; p-value<0.01. CXCL12 [pg/ml] 6000 ** 4000 2000 + siR N A 0 Supplemental Figure 17: HS-5 cells transfected with CXCL12 siRNA were cultured for 24 hours upon transfection and the CXLC12 secretion assessed (as compared to non-transfected cells) by ELISA. The bars represent the standard error of the mean. Abbreviations: *; pvalue<0.05, **; p-value<0.01, ***; p-value<0.001. 16
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