Context-dependent modification of PFKFB3 in hematopoietic stem cells promotes anaerobic glycolysis and ensures stress hematopoiesis

  1. Shintaro Watanuki
  2. Hiroshi Kobayashi  Is a corresponding author
  3. Yuki Sugiura  Is a corresponding author
  4. Masamichi Yamamoto
  5. Daiki Karigane
  6. Kohei Shiroshita
  7. Yuriko Sorimachi
  8. Shinya Fujita
  9. Takayuki Morikawa
  10. Shuhei Koide
  11. Motohiko Oshima
  12. Akira Nishiyama
  13. Koichi Murakami
  14. Miho Haraguchi
  15. Shinpei Tamaki
  16. Takehiro Yamamoto
  17. Tomohiro Yabushita
  18. Yosuke Tanaka
  19. Go Nagamatsu
  20. Hiroaki Honda
  21. Shinichiro Okamoto
  22. Nobuhito Goda
  23. Tomohiko Tamura
  24. Ayako Nakamura-Ishizu
  25. Makoto Suematsu
  26. Atsushi Iwama
  27. Toshio Suda
  28. Keiyo Takubo  Is a corresponding author
  1. Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Japan
  2. Division of Hematology, Department of Medicine, Keio University School of Medicine, Japan
  3. Department of Cell Fate Biology and Stem Cell Medicine, Tohoku University Graduate School of Medicine, Japan
  4. Department of Biochemistry, Keio University School of Medicine, Japan
  5. Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Japan
  6. Department of Research Promotion and Management, National Cerebral and Cardiovascular Center, Japan
  7. Department of Life Sciences and Medical BioScience, Waseda University School of Advanced Science and Engineering, Japan
  8. Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, Japan
  9. Department of Immunology, Yokohama City University Graduate School of Medicine, Japan
  10. Advanced Medical Research Center, Yokohama City University, Japan
  11. Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Japan
  12. International Research Center for Medical Sciences, Kumamoto University, Japan
  13. Center for Advanced Assisted Reproductive Technologies, University of Yamanashi, Japan
  14. Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Japan
  15. Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Japan
  16. Department of Microscopic and Developmental Anatomy, Tokyo Women's Medical University, Japan
  17. Live Imaging Center, Central Institute for Experimental Animals, Japan
  18. Cancer Science Institute of Singapore, National University of Singapore, Singapore
35 figures, 1 table and 7 additional files

Figures

Figure 1 with 3 supplements
HSC cell cycling increases overall glycolytic flux, but not flux into mitochondria.

(A) Experimental design used for glucose isotope tracer analysis in HSCs from 5-FU- or PBS-treated mice. (B) Heat map of metabolite levels in HSCs derived from mice treated with PBS or 5-FU. (C–F) The semi-quantitative value (10–6 µM) of U-13C6-glucose-derived metabolites in glycolysis (C), the first round of TCA cycle (D), the PPP, and nucleotide synthesis (F) in HSCs from 5-FU- or PBS-treated mice (PBS group = 1.0); In (B)-(F), biological replicates from the PBS and 5-FU groups, obtained on three separate days, were pooled, analyzed by IC-MS, quantified based on calibration curve data for each metabolite (see ‘Ion chromatography mass spectrometry (IC-MS) analysis’ section in ‘Materials and methods’ for details). (G–H) A Mito Stress test with the Seahorse flux analyzer on HSCs derived from mice treated with PBS or 5-FU; ECAR (G) and OCR (H) before and after oligomycin treatment. (Data were obtained from n=7 technical replicates for PBS-treated HSCs and n=6 for 5-FU-treated HSCs.) (I) Experimental schema of in vivo 2-NBDG analysis. (J) Representative histograms of 2-NBDG analysis (gray: no 2-NBDG, red: PBS group, blue: 5-FU group). (K) 2-NBDG positivity in each fraction; data represent four pooled biological replicates for the PBS group and three for the 5-FU group; MyP: myeloid progenitor. (L) EPCR expression and 2-NBDG positivity within HSC fractions. Data were extracted from each individual in (K). Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined by Student’s t-test (C–F, G–H when comparing the PBS and 5-FU groups, and K–L) or paired-samples t-test (G–H when comparing the conditions before and after exposure to oligomycin within the PBS/5-FU group). Abbreviations: G6P, glucose-6-phosphate; F6P, fructose-6-phosphate; F1,6BP, fructose-1,6-bisphosphate; G3P, glycerol-3-phosphate; DHAP, dihydroxyacetone phosphate; 3 PG, 3-phosphoglycerate; 2 PG, 2-phosphoglycerate; PEP, phosphoenolpyruvate; PYR, pyruvate; LAC, lactate; Ac-CoA; acetyl-CoA; CIT, citrate; ACO, cis-aconitic acid, isocitrate; 2OG, 2-oxoglutarate; SUC, succinate; FUM, fumarate; MAL, malate; OAA, oxaloacetate; 6 PG, glucose-6-phosphate; Ru5P, ribulose-5-phosphate; Xu5P, xylulose-5-phosphate; R5P, ribose-5-phosphate; S7P, sedoheptulose-7-phosphate; E4P, erythrose-4-phosphate; PRPP, phosphoribosyl pyrophosphate; IMP, inosine monophosphate; ATP, adenosine triphosphate; GTP, guanine triphosphate; UMP, uridine monophosphate; UTP, uridine triphosphate; TTP, thymidine triphosphate. See also Figure 1—figure supplements 13.

Figure 1—figure supplement 1
Dependence on glycolysis increases with cell cycle progression of HSCs.

(A) Schematic illustration of 5-FU administration and analysis. (B) Representative staining plot of BM cells derived from mice 5 d (day 6) after treatment with PBS or 5-FU (day 1); note the gating of c-Kit high-dim cells in the LSK staining. Because the same BMMNC counts were obtained for each group, the Flt3-negative gated dot plot (bottom-right) for the 5-FU group appears to show an increase in the HSC fraction. (C) Contour plot of c-Kit expression in Lin-Sca-1+EPCR+CD150+CD48- cells from mice five days after PBS or 5-FU administration. (D) Frequency of Ki67-positive and -negative HSCs after 5-FU administration. n=5 biological duplicates for each group. (E) Changes in ATP concentration in HSCs after 5-FU administration (n>70 single HSCs for each group). Data are representative results of pooled samples of two biological replicates. (F) Ki-67 positivity in HSCs by route of 5-FU administration (i.p. or i.v.). n=4 biological duplicates for each group. (G–H) Intracellular staining of pRb in EPCR+ or EPCR- HSCs derived from PBS- or 5-FU-treated mice. Representative plot of pRb and DNA content in EPCR+ HSCs from both groups (G). Summary of results (H). n=3 biological duplicates for each group. (I–K) Analysis of mVenus-p27K- mice treated with PBS or 5-FU. Experimental schema (I). Representative G0 marker distribution in HSC in PBS (blue) or 5-FU (red) groups (J). Percentage of G0 marker-positive cells in total HSCs and EPCR+ or EPCR- HSCs in PBS (blue bars) or 5-FU group (red bars) (K). n=4–5 biological replicates for each group. The data for each panel is extracted from the same individual. (L) In vitro 2-NBDG assay. cyto: cytochalasin, phlo: phloretin. n=three biological replicates for each group. (M) In vivo administration of 2-NBDG followed by the Ki67/Hoechst 33432 staining of HSCs. n=six biological replicates for each group. (N) Relative percentage of HSCs remaining after culture under quiescence-maintaining or proliferative conditions in the presence of oligomycin. HSC number for the control (Ctl) vehicle (DMSO)-treated group was set to 100%; n=4 technical replicates for each group. The data are representative results from three independent experiments. (See ‘MACSQuant analysis of cell number’ under ‘Materials and methods’ for more information.). Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined using Student’s t-test (H, K, N) or one-way ANOVA followed by Tukey’s test (D–F, and L–M).

Figure 1—figure supplement 2
antified metabolite pool in HSCs under quiescence, proliferation, or OXPHOS-inhibition.

(A) Comparison of metabolite levels in c-Kit enriched cells pre- and post-sorting. n=3 biological replicates for each group. ND: not detected. (B) Metabolic overview of U-13C6-glucose tracing among pathways related to glycolysis, PPP, NAS, and the TCA cycle in HSCs from 5-FU- (blue) or PBS-treated (red) mice, and DMSO- (black) or oligomycin (Oligo)-treated (orange) HSCs. Fates of carbons derived from U-13C6-glucose in each metabolite are shown as yellow circles. Each graph indicates relative amounts of U-13C6-glucose-derived metabolites. (C–E) Ratio of U-13C6-glucose-labelled to non-labelled metabolites in glycolysis (C), the first round of the TCA cycle (D), and the PPP plus nucleic acid synthesis (E) in PBS- (red bars) and 5-FU-treated (blue bars) HSCs. (F–H) Ratio of U-13C6-glucose-labelled to non-labelled metabolites in glycolysis (F), the first round of the TCA cycle (G), and the PPP plus nucleic acid synthesis (H) in HSCs treated with vehicle (black bars) or oligomycin (orange bars). In (B–H), data are extracted from three biological replicates for HSCs derived from PBS- or 5-FU-treated mice and from four for HSCs after DMSO or oligomycin treatment. Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined using two-way ANOVA with Sidak’s test (A) and Student’s t-test (B) by comparing PBS and 5-FU groups or DMSO and oligomycin groups. Abbreviations: G6P, glucose-6-phosphate; F6P, fructose-6-phosphate; F1,6BP, fructose-1,6-bisphosphate; G3P, glycerol-3-phosphate; DHAP, dihydroxyacetone phosphate; 3 PG, 3-phosphoglycerate; 2 PG, 2-phosphoglycerate; PEP, phosphoenolpyruvate; PYR, pyruvate; LAC, lactate; Ac-CoA; acetyl-CoA; CIT, citrate; ACO, cis-aconitic acid, isocitrate; 2OG, 2-oxoglutarate; SUC, succinate; FUM, fumarate; MAL, malate; OAA, oxaloacetate; 6 PG, glucose-6-phosphate; Ru5P, ribulose-5-phosphate; Xu5P, xylulose-5-phosphate; R5P, ribose-5-phosphate; S7P, sedoheptulose-7-phosphate; E4P, erythrose-4-phosphate; PRPP, phosphoribosyl pyrophosphate; IMP, inosine monophosphate; ATP, adenosine triphosphate; GTP, guanine triphosphate; UMP, uridine monophosphate; UTP, uridine triphosphate; TTP, thymidine triphosphate.

Figure 1—figure supplement 3
Mito Stress test results using the Seahorse flux analyzer.

(A–D) Overview of the Mito Stress test on the Seahorse flux analyzer for PBS- or 5-FU-treated HSCs (A) ECAR, (B) OCR and HSCs or MyPs (C) ECAR, (D) OCR.

OXPHOS inhibition activates compensatory glycolysis in HSCs.

(A) Experimental design used for glucose isotope tracer analysis in HSCs treated with the OXPHOS inhibitor oligomycin. (B) Heat map of metabolite levels detected by in vitro tracer analysis of U-13C6-glucose in HSCs treated with DMSO or oligomycin (Oligo). (C–F) Relative amounts of U-13C6-glucose-derived metabolites in glycolysis (C), the first round of TCA cycle (D), the PPP(E), and nucleotide synthesis (F) in DMSO- (black) or oligomycin-treated (orange) HSCs; In (B)-(F), biological replicates of the DMSO and oligomycin groups obtained on four separate days were pooled, analyzed by IC-MS, and quantified based on calibration curve data for each metabolite (see ‘Ion chromatography mass spectrometry (IC-MS) analysis’ section in ‘Materials and methods’ for details). (G–H) Mito Stress test on the Seahorse flux analyzer for HSC and MyPs; ECAR (G) and OCR (H) before and after oligomycin treatment. (Data were obtained from n=3 technical replicates for HSCs and n=10 technical replicates for MyPs.). Data are shown as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined by paired-samples t-test (C-E and G–H). Abbreviations: G6P, glucose-6-phosphate; F6P, fructose-6-phosphate; F1,6BP, fructose-1,6-bisphosphate; G3P, glycerol-3-phosphate; DHAP, dihydroxyacetone phosphate; 3 PG, 3-phosphoglycerate; 2 PG, 2-phosphoglycerate; PEP, phosphoenolpyruvate; PYR, pyruvate; LAC, lactate; Ac-CoA; acetyl-CoA; CIT, citrate; ACO, cis-aconitic acid, isocitrate; 2OG, 2-oxoglutarate; SUC, succinate; FUM, fumarate; MAL, malate; OAA, oxaloacetate; 6 PG, glucose-6-phosphate; Ru5P, ribulose-5-phosphate; Xu5P, xylulose-5-phosphate; R5P, ribose-5-phosphate; S7P, sedoheptulose-7-phosphate; E4P, erythrose-4-phosphate; PRPP, phosphoribosyl pyrophosphate; IMP, inosine monophosphate; ATP, adenosine triphosphate; GTP, guanine triphosphate; UMP, uridine monophosphate; UTP, uridine triphosphate; TTP, thymidine triphosphate. See also Figure 1—figure supplements 13.

Figure 3 with 2 supplements
Quantitative 13C-MFA of quiescent, proliferative, and stressed HSCs.

(A–C) Overview of quantitative 13C-MFA of PBS-treated HSCs (A), 5-FU-treated HSCs (B), and OXPHOS-inhibited HSCs (C). The representative net flux for each reaction with glucose uptake as 100 is shown in the squares below the catalytic enzymes for each reaction listed in green letters. Red arrows indicate reactions with particularly elevated fluxes and blue arrows indicate reactions with particularly decreased fluxes. (D) Heatmap of the relative flux of each enzyme in the 5-FU or oligomycin groups compared to that in the quiescent (Ctl) HSC (The metabolic flux of each enzyme in the Ctl group was standardized as 100.). (E–J) Fluxes due to reactions with PFK (E, H), G6PD (F, I), and PDH (G, J). Fluxes of HSCs derived from mice treated with 5-FU (blue bars) or PBS (red bars) (D–F) and of HSCs treated with DMSO (black bars) or oligomycin (orange bars) (G–I) are shown. Data is obtained from 100 simulations in OpenMebius, and flux data for each enzyme is displayed (Supplementary file 4). (K–L) Ratio of fructose 1,6-bisphosphate (F1,6BP) to fructose-6-phosphate (F6P) calculated from tracer experiments shown in Figure 1B and Figure 2B. Effects of 5-FU administration (K) or mitochondrial inhibition by oligomycin (L) are summarized. Data are shown as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined by Student’s t-test (E–L). Abbreviations: HK, hexokinase; PGI, glucose-6-phosphate isomerase; PFK, phosphofructokinase; TPI, triose phosphate isomerase; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; PGM, phosphoglycerate mutase; PK, pyruvate kinase; LDH, lactate dehydrogenase; PC, pyruvate carboxylase; PDH, pyruvate dehydrogenase; CS; citrate synthase; IDH, isocitrate dehydrogenase; αKGDH, α-ketoglutaric acid dehydrogenase; SDH, succinate dehydrogenase; G6PD, glucose-6-phosphate dehydrogenase; TAL, transaldolase. See also Figure 3—figure supplements 12.

Figure 3—figure supplement 1
Quantitative 13C-MFA of HSCs under quiescence, proliferation, and OXPHOS inhibition.

(A–C) Enzyme reaction flux values for each simulation (100 times in total) in PBS-treated (A), 5-FU-treated (B), and OXPHOS-inhibited HSCs (C). Flux values calculated in the same simulation are connected by lines; note the small variation in flux values calculated in different simulations in 5-FU-treated (B) or OXPHOS-inhibited HSCs (C) compared to that in PBS-treated HSCs (A). (D–U) Fluxes of each reaction determined using quantitative 13C-MFA in HSCs from mice treated with 5-FU (blue bars) or PBS (red bars) (D–L), or in HSCs after treatment with vehicle (black bars) or oligomycin (orange bars) (M–U). The net flux was calculated when the glucose uptake was set at 100. The name of the enzyme catalyzing each reaction is listed above the graph. Each gray dot represents the estimated flux obtained from 100 mathematical simulations. (See ‘Quantitative 13C-MFA with OpenMebius’ under ‘Materials and methods’ for more information.). Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined using Student’s t-test (D–U). Abbreviations: HK, hexokinase; PGI, glucose-6-phosphate isomerase; PFK, phosphofructokinase; TPI, triose phosphate isomerase; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; PGM, phosphoglycerate mutase; PK, pyruvate kinase; LDH, lactate dehydrogenase; PC, pyruvate carboxylase; PDH, pyruvate dehydrogenase; CS; citrate synthase; IDH, isocitrate dehydrogenase; αKGDH, α-ketoglutaric acid dehydrogenase; SDH, succinate dehydrogenase; G6PD, glucose-6-phosphate dehydrogenase; TAL, transaldolase.

Figure 3—figure supplement 2
Quantified metabolite pool in HSCs from PBS- or 5-FU-treated mice.

(A) Experimental schema. (B–D) Heat maps of the glycolytic system (B), TCA cycle (C), PPP and NAS and glutathione labeling rates (D). (E–I) Labeling rates of Asp M+2 (E), Glu M+2 (F), IMP M+5 (G), ATP M+5 (H), and reduced glutathione M+2 (I) in PBS- (blue bars) or 5-FU-treated HSCs (red bars). (J) Percentage of total 13C labeled body mass of glycolysis, TCA cycle, PPP, and NAS detected in PBS-treated or 5-FU-treated HSCs. HSCs derived from one or two mice in the PBS group and two or three mice in the 5-FU group were pooled. n=4 biological replicates for each group. (See ‘Preparation and storage of in vivo U-13C6-glucose tracer samples’ in ‘Materials and methods’ for details.) Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined using Student’s t-test (E–J). Abbreviations: G6P, glucose-6-phosphate; F6P, fructose-6-phosphate; F1,6BP, fructose-1,6-bisphosphate; G3P, glycerol-3-phosphate; DHAP, dihydroxyacetone phosphate; 3 PG, 3-phosphoglycerate; 2 PG, 2-phosphoglycerate; PEP, phosphoenolpyruvate; PYR, pyruvate; LAC, lactate; CIT, citrate; ISOCIT; isocitrate; 2OG, 2-oxoglutarate; SUC, succinate; FUM, fumarate; MAL, malate; 6 PG, glucose-6-phosphate; Ru5P, ribulose-5-phosphate; Xu5P, xylulose-5-phosphate; R5P, ribose-5-phosphate; S7P, sedoheptulose-7-phosphate; PRPP, phosphoribosyl pyrophosphate; IMP, inosine monophosphate; ATP, adenosine triphosphate; Asp, Aspartic acid; Glu, Glutamate.

Figure 4 with 2 supplements
PFKFB3 activates the glycolytic system in proliferating HSCs.

(A) Experimental design used to conduct real-time ATP analysis of HSCs treated with 5-FU or PBS. PLFA medium containing mitochondrial substrates (pyruvate, lactate, fatty acids, and amino acids) but no glucose, was used for experiments with 2-DG; Ba-M containing neither mitochondrial substrates nor glucose was used for experiments with oligomycin, PFKFB3 inhibitor, or AMPK inhibitor. (B–E) Results of real-time ATP analysis of PBS- (red) or 5-FU-treated (blue) HSCs after treatment with 2-DG (B, D), oligomycin (C, E). (F) Normalized mRNA counts of PFKFB isozymes based on the RNA sequencing of HSCs. (G-J) Results of real-time ATP analysis of PBS- (red) or 5-FU-treated (blue) HSCs after treatment with PFKFB3 inhibitor (G, I), or AMPK inhibitor (H, J). Bar graphs show corrected ATP concentrations for the last 2 min (D) of (B), 6–7 min (E) of (C), or the last 1 min (I, J) of (G, H) for PFKFB3 and AMPK inhibitors, respectively. Each group represents at least 60 cells. Data are representative results of pooled samples from three biological replicates. (see ‘Time-course analysis of FRET values’ in ‘Materials and methods’ for details of the correction method used to calculate ATP concentration.) Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined by Student’s t-test (D, E, I, and J) or a one-way ANOVA followed by Tukey’s test (F). See also Figure 4—figure supplements 12.

Figure 4—figure supplement 1
Establishment of a real-time ATP concentration analysis system using GO-ATeam2.

(A) Representative plot of HSPC fractions from GO-ATeam2 +mice. The identified fractions are shown at the top of the graph and the upper gating of that fraction is shown in parentheses. (B–C) Number of BMMNCs derived from C57BL/6J and GO-ATeam2 mice (B) and percentage of each fraction present (C). (D) Schematic diagram showing effects of key metabolic pathways and regulators (orange) and their inhibitors (red). (E) Transformation of time-course plot of ATP concentration in individual HSCs from GO-ATeam2 mice (left) to a planar curve after fitting (right). (F) Time-course analysis of ATP concentration in HSCs from GO-ATeam2 mice in basal medium (Ba-M) without pre-saturation plus various indicated additives. (G–H) Effects of indicated metabolites on ATP concentration of HSCs (G) or MyPs (H) in Ba-M. (I) Apoptosis assay results for HSCs exposed to 2-DG (50 mM) or oligomycin (1 µM) for 10 min. n=3 biological replicates. Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined using Student’s t-test (B), two-way ANOVA with Sidak’s test (C), or one-way ANOVA followed by Tukey’s test (I).

Figure 4—figure supplement 2
FAO is not active in proliferating HSCs.

(A–H) Results of real-time ATP analysis of PBS- (red) or 5-FU-treated (blue) HSCs (two-days (A–D) or 14 days (E–H) after PBS/5-FU administration) after treatment with 2-DG (A, C, E, G) or oligomycin (B, D, F, H). Bar graphs show corrected ATP concentrations for the last 30 s of the analysis. Each group represents at least 28 cells. Data are representative results of pooled samples from two biological replicates. (see ‘Time-course analysis of FRET values’ in ‘Materials and methods’ for details on the correction method used to calculate the ATP concentration.) (I) Average amount of ATP per cell. The amount of ATP detected in the luciferase assay was divided by the number of HSCs used in the analysis. n=three biological replicates for each group. (J–M) Results of the real-time ATP analysis of PBS- (J, K) or 5-FU-treated (L, M) HSCs after treatment with etomoxir (100 µM) and/or DON (2 mM). Bar graphs show corrected ATP concentrations for the last 1 min of the analysis. Each group represents at least 60 cells. Data are representative results of pooled samples from two biological replicates. (N) MFI of FAOBlue. As a negative control, HSCs were exposed to etomoxir (100 µM). (O–P) Effects of DMSO (Ctl, red line), DON (2 mM, blue lines), etomoxir (100 µM, green lines) on ATP in HSCs in the presence of 200 mg/dL glucose. Dashed lines are ATP concentrations with additional AZ PFKFB3 26. Data are presented as the mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined using a Student’s t-test (C, D, G, H, and I), or one-way ANOVA followed by Tukey’s test (K, M, N, and P).

Figure 5 with 1 supplement
PFKFB3 accelerates glycolysis in HSCs under OXPHOS inhibition in an AMPK-dependent manner.

(A) Experimental design of real-time ATP analysis using GO-ATeam2 knock-in BMMNCs. Ba-M was used in experiments with oligomycin. For other experiments, PLFA medium was used. (B–C) Evaluation of factors affecting ATP concentration in HSCs (B) and GMPs (C) based on the GO-ATeam2 system. GO-ATeam2 knock-in BMMNCs were incubated with glucose, oligomycin, 2-DG, or glucose plus oligomycin, and the FRET/EGFP ratio was calculated. (D) ATP concentration in indicated stem/progenitor fractions in PLFA medium (red bars) alone or PLFA medium plus 2-DG (blue bars). ATP concentration for the last 2 min of the analysis time is shown. Data is summarized from Figure 5B–C and Figure 5—figure supplement 1A–D. Each group represents at least 110 cells. Data are representative results of pooled samples from three biological replicates. (E) ATP concentration in indicated stem/progenitor fractions in Ba-M plus glucose (dark blue bars) or Ba-M plus glucose and oligomycin (orange bars). ATP concentration for the last 1 min of the analysis period is shown. Data is summarized from Figure 5B–C and Figure 5—figure supplement 1A–D. Each group represents at least 43 cells. Data are representative results of pooled samples from three biological replicates. (F–I) Effects of PFKFB3 or AMPK inhibitors (PFKFB3i or AMPKi, respectively) on ATP concentration in HSCs from GO-ATeam2 mice in Ba-M plus glucose only (F) or Ba-M plus glucose and oligomycin (G). ATP concentrations for the last 1 min of the analysis period are shown in (H) and (I) for glucose only and glucose with oligomycin groups, respectively. Each group represents at least 90 cells. Data are representative results of pooled samples from three biological replicates. (J) Experimental schema for cell cycle assay and real-time ATP concentration analysis after overexpression of Pfkfb3. (K) Cell cycle status of Pfkfb3-overexpressing (Pfkfb3OE) and mock-transduced HSCs. (L–M) Effects of inhibitors on ATP concentration in Pfkfb3-overexpressing GO-ATeam2+ HSCs. Cells were exposed to vehicle or 2-DG (L), oligomycin in the presence or absence of glucose 12.5 mg/dL (M), and ATP concentrations for the last 2 min (L) or 1 min (M) of the analysis period were calculated. Data are representative results of pooled samples from three biological replicates. Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined by Student’s t-test (D, E, and K) or one-way ANOVA followed by Tukey’s test (H, I, L, and M). See also Figure 5—figure supplement 1.

Figure 5—figure supplement 1
Steady-state PFKFB3 activity defines HSC and HPC metabolic kinetics and cell cycle.

(A–D) Evaluation of factors affecting ATP concentration in MPPs (A), MEPs (B), CMPs (C), and CLPs (D) based on the GO-ATeam2 system. GO-ATeam2-knock-in BMMNCs were incubated with glucose, oligomycin, 2-DG, or glucose plus oligomycin, and the FRET/EGFP ratio was calculated. (E) Effects of DMSO (Ctl, red line), oligomycin (1 µM, blue lines), FCCP (2 µM, green lines), and rotenone (1 µM, orange lines) on ATP in HSCs. Dashed lines are ATP concentrations with additional ddH2O and solid lines are ATP concentrations when 200 mg/dL glucose is added. (F) ATP concentration during the last 1 min in (E). Data are representative results for pooled samples of two biological replicates. (G) Effects of indicated concentrations of glucose (mg/dL) on ATP concentration in oligomycin-treated or control HSCs (left panel), or in MyPs (right panel) in PLFA medium. (H–K) Effects of inhibitors of PKM2 or LKB1 (PKM2i or LKB1i, respectively) on ATP concentration of HSCs from GO-ATeam2 mice in Ba-M with either glucose (Glc) or glucose plus oligomycin. ATP concentrations for the last 2 min of analysis time are summarized in (J) and (K), respectively. Each group represents at least 50 cells. Data are the result of one experiment. (L) Composition of adenine phosphates (AMP, ADP, and ATP) in HSCs treated with oligomycin (Oligo), or HSCs from 5-FU-treated mice (5-FU) and control HSCs (Ctl; no treatment or DMSO-treated). Data show results of tracer experiments shown in Figure 1 and Figure 2. (M–P) Effects of a PFKFB3 inhibitor (PFKFB3i) on ATP concentration in GMPs (M), MEPs (N), CMPs (O), or CLPs (P) from GO-ATeam2 mice in Ba-M treated with glucose (Glc) plus vehicle (red lines), glucose plus PFKFB3i (blue lines), or glucose plus oligomycin plus PFKFB3i (green lines). (Q) ATP concentration in indicated progenitor fractions in Ba-M with vehicle (red bars) or PFKFB3 inhibitor (dark blue bars). ATP concentrations for the last 1 min of the analysis period are shown. Data is summarized from Figure 5—figure supplement 1M–P. Each group represents at least 350 cells. Data are representative results of pooled samples from two biological replicates. (R–U) Effects of inhibitors on ATP concentration in Pfkfb3-overexpressing GO-ATeam2+ HSCs. Cells were exposed to vehicle (Ctl) (R), 2-DG (S), oligomycin (T), or glucose 12.5 mg/dL and oligomycin (U). Data are representative results of pooled samples from two biological replicates. Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined using Student’s t-test (F, Q) or one-way ANOVA followed by Tukey’s test (J–L).

Figure 6 with 1 supplement
PFKFB3 methylation by PRMT1 enables ATP production by cell-cycling HSCs.

(A) Normalized Pfkfb3 mRNA counts based on RNA sequencing of PBS-treated (red) or 5-FU-treated (blue) HSCs. Data are representative results of pooled samples from three biological replicates. Data were extracted from the same pooled samples as in Figure 4J and Figure 6—figure supplement 1. (B) Quantification of mean fluorescent intensity (MFI) of PFKFB3 protein in PBS- or 5-FU-treated HSCs. The lower part of the graph shows representative images of immunocytochemistry of PFKFB3 in each group. n=26–27 single HSCs for each group. The data are representative results from two independent experiments. (C) Quantification of MFI of phosphorylated-PFKFB3 (p-PFKFB3) protein in PBS- or 5-FU-treated HSCs. The lower part of the graph shows representative images of immunocytochemistry of p-PFKFB3 in each group. n=27 single HSCs for each group. The data are representative results from two independent experiments. (D) Quantification of mean fluorescence intensity (MFI) of p-PFKFB3 in HSCs treated with glucose (200 mg/dL); glucose plus oligomycin (1 µM); and glucose, oligomycin, and dorsomorphin (100 µM) for 5 min. The lower part of the graph shows representative images of immunocytochemistry of p-PFKFB3 in each group. n=32–36 for each group. The data are representative results from two independent experiments. (E) Normalized Prmt1 mRNA counts based on RNA sequencing of PBS-treated (red) or 5-FU-treated (blue) HSCs. Data are representative results of pooled samples from three biological replicates. (F) MFI quantification of methylated-PFKFB3 (m-PFKFB3) in PBS- or 5-FU-treated HSCs. The lower part of the graph shows representative images of immunocytochemistry of m-PFKFB3 in each group. n=23–41 for each group. The data are representative results from three independent experiments. (G) Quantification of MFI of m-PFKFB3 in PBS- or 5-FU-treated HSCs or 5-FU-treated HSCs after 15 min treatment with a PRMT1 inhibitor (90 μg/mL GSK3368715); n=25–35 single HSCs for each group. The lower part of the graph shows representative images showing immunocytochemistry of m-PFKFB3. Data represent a single experiment. (H) Quantitation of m-PFKFB3 in NBDG-positive or -negative HSCs in mice treated with PBS or 5-FU. The lower part of the graph shows representative images of immunocytochemistry of m-PFKFB3 in each group. n=28–41 for each group. The data are representative results from two independent experiments. (I) Corrected ATP levels in PBS- (red) or 5-FU-treated (blue) HSCs 15 min after treatment with vehicle or a PRMT1 inhibitor (90 µg/mL GSK3368715). Each group represents at least 101 cells. Data are representative results of pooled samples of two biological replicates. (see ‘Time-course analysis of FRET values’ in ‘Materials and methods’ for details of the correction method used to calculate ATP concentration.) (J) ATP concentration in mock-transduced (Ctl) or Pfkfb3-overexpressed (OE) HSCs after treatment with the PRMT1 inhibitor (90 µg/mL GSK3368715). ATP concentration for the last 1 min of the analysis period is shown. Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined by Student’s t-test (A-C, E-F, and I-J) or one-way ANOVA followed by Tukey’s test (D, G, and H). See also Figure 6—figure supplement 1.

Figure 6—figure supplement 1
ene expression related to Prmt1 in proliferating HSCs.

Data are presented as the mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined using a Student’s t-test.

Figure 7 with 1 supplement
PFKFB3 maintains HSC function under proliferative stress.

(A–C) Transplant analysis of Pfkfb3-KO or Pfkfb3CA-overexpressing HSCs. Experimental design (A). PB chimerism of donor-derived cells at 4 months post-transplant. Pfkfb3-KO group, n=6; Rosa26-KO group, n=4; (B) Pfkfb3 group, n=5; pMY-IRES-GFP group, n=4. (C) The data are representative results from two independent experiments. (D–E) 5-FU administration after bone marrow reconstruction with Pfkfb3- or Rosa26-KO HSPCs. Experimental schema (D). Behavior of the Pfkfb3- or Rosa26-KO cells in PB after 5-FU administration (E). n=5 for each group. (F–K) Cell cycle analysis and apoptosis assay of Pfkfb3- or Rosa26-KO HSPCs on day 2 post-BMT. Experimental schema (F). Representative plots of Ki67/Hoechst33432 staining of Rosa26-KO (G) or Pfkfb3-KO (H) HSPCs and summary of analysis (I); summary of in vivo BrdU labeling assay (J). Apoptosis assay results (K). n=4–5 biological replicates for each group. (L–N) Cell cycle analysis of Pfkfb3CA or Mock-overexpressing HSPCs on day 2 after BMT. Experimental Schema (L). Representative plot of Ki67/Hoechst33432 staining for both groups (M) and summary of analysis (N). n=5 biological replicates for each group. (O) Models showing ATP production and regulation in quiescent, OXPHOS-inhibited, and cell-cycling HSCs. Note that the GO-ATeam2 system identified plastic acceleration of glycolysis by PFKFB3 in response to different types of stress maintains ATP levels. Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined by Student’s t-test (B, C, E, I-K, and N). See also Figure 7—figure supplement 1.

Figure 7—figure supplement 1
PFKFB3 contributes to HSC proliferation and differentiation in vitro.

(A–D) Effects of in vitro PFKFB3 inhibition, KO, or overexpression on HSCs. Experimental design (A). Number of cells in an HSC-derived colony following exposure to a PFKFB3 inhibitor (PFKFB3i) at indicated concentrations (B) or after Pfkfb3 KO by CRISPR-Cas9 (C); n=4 technical replicates for each group. Control groups were vehicle (DMSO)-treated (B) or CD45 KO (C). (D) In vitro effect of Pfkfb3-overexpression on HSCs. Number of cells in Pfkfb3-overexpressing or mock (pMY-IRES-GFP)-transduced HSC-derived colonies; n=4 technical replicates for each group. (B–D) are representative results of two or three independent experiments. (E–F) KO efficiency evaluated by sgRNA (E) or triple gRNA (F). The indel spectrum (horizontal axis) and the percentage of each indel (vertical axis) are shown. (G) qPCR results for Pfkfb3 expression in validation experiments of mock- (black bar) or Pfkfb3CA- (red bar) overexpression. n=4 technical replicates for each group. (H) Analysis of the homing efficiency and GFP+ blood cells in recipient BM 16 hr after the transplantation of Rosa26- or Pfkfb3-KO GFP+ HSPCs. Data are presented as mean ± SD. * p≤0.05, ** p≤0.01, *** p≤0.001 as determined using Student’s t-test (C, D, G, and H) or one-way ANOVA followed by Tukey’s test (B).

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Tables

Appendix 1—key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Strain, strain background (Mus musculus, male and female)C57BL/6JJmsSlc Ly5.2+Japan SLC (Shizuoka, Japan)N/A
Strain, strain background (Mus musculus, male and female)C57BL/6J-Ly5.1CLEA Japan (Shizuoka, Japan)N/AUtilized for hematopoietic cell transplantation studies to distinguish donor and recipient cells.
Strain, strain background (Mus musculus, male and female)GO-ATeam2 miceGenerated in Yamamoto laboratoryN/AUsed for ATP analysis
Strain, strain background (Mus musculus, male and female)Ubc-GFP miceThe Jackson LaboratoryStock No: 007076
Strain, strain background (Mus musculus, male and female)mVenus-p27K- miceProvided by Kitamura LaboratoryN/AUsed for cell cycle analysis
AntibodyAnti-mouse CD4-PerCP-Cy5.5
(clone: RM4-5, rat monoclonal)
TONBO biosciencesCat# 65–0042 U100; RRID: AB_2621876(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse CD8a-PerCP-Cy5.5
(clone: 53–6.7, rat monoclonal)
TONBO biosciencesCat# 65–0081 U100; RRID: AB_2621882(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse B220-PerCP-Cy5.5
(clone: RA3-6B2, rat monoclonal)
TONBO biosciencesCat# 65–0452 U100; RRID: AB_2621892(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse B220-APC
(clone: RA3-6B2, rat monoclonal)
BioLegendCat# 103212; RRID: AB_312997(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse Ter-119-PerCP-Cy5.5
(clone: TER-119, rat monoclonal)
TONBO biosciencesCat# 65–5921 U100(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse Gr1 (Ly-6G/6 C)-PerCP-Cy5.5
(clone: RB6-8C5, rat monoclonal)
BioLegendCat# 108428; RRID: AB_893558(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse Gr1-PE-Cy7
(clone: RB6-8C5, rat monoclonal)
TONBO biosciencesCat# 60–5931 U100; RRID: AB_2621870(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse Mac1 (CD11b)-PerCP-Cy5.5
(clone: M1/70, rat monoclonal)
TONBO biosciencesCat# 65–0112 U100; RRID: AB_2621885(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse Mac1-PE-Cy7
(clone: M1/70, rat monoclonal)
TONBO biosciencesCat# 60–0112 U100; RRID: AB_2621836(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse CD45.1-PE
(clone: A20, mouse monoclonal)
BD biosciencesCat# 553776; RRID: AB_395044(1 µL/mouse)
AntibodyAnti-mouse CD45.1-Alexa Fluor700
(clone: A20, mouse monoclonal)
BioLegendCat# 110724; RRID: AB_493733(1 µL/mouse)
AntibodyAnti-mouse CD45.2-FITC
(clone: 104, mouse monoclonal)
BD biosciencesCat# 553772; RRID: AB_395041(1 µL/mouse)
AntibodyAnti-mouse Sca-1 (Ly-6A/E)-PE-Cy7
(clone: E13-161.7, rat monoclonal)
BioLegendCat# 122514; RRID: AB_756199(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse c-Kit (CD117)-APC-Cy7
(clone: 2B8, rat monoclonal)
BioLegendCat# 105826; RRID: AB_1626278(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyCD117 MicroBeads MouseMiltenyi BiotecCat# 130-091-224(1:5)
AntibodyAnti-mouse CD150-PE
(clone: TC15-12F12.2, rat monoclonal)
BioLegendCat# 115904; RRID: AB_313683(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse CD150-BV421
(clone: TC15-12F12.2, rat monoclonal)
BioLegendCat# 115926; RRID: AB_2562190(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse CD150-APC
(clone: TC15-12F12.2, armenian hamster monoclonal)
BioLegendCat# 115910; RRID: AB_ 493460(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse CD48-FITC
(clone: HM48-1, armenian hamster monoclonal)
BioLegendCat# 103404; RRID: AB_313019(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse CD48-APC
(clone: HM48-1, qrmenian hamster monoclonal)
BioLegendCat# 103411; RRID: AB_571996(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse CD48-BV510
(clone: HM48-1, armenian hamster monoclonal)
BD biosciencesCat# 563536(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse CD48-Alexa Fluor700
(clone: HM48-1, armenian hamster monoclonal)
BioLegendCat# 103426
RRID: AB_10612754
(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-mouse CD41-APC
(clone: MWReg30, rat monoclonal)
BioLegendCat# 133914; RRID: AB_11125581(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-CD34-BV421
(clone: RAM34, rat monoclonal)
BD biosciencesCat# 562608; RRID: AB_11154576(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-CD34-FITC
(clone: RAM34, rat monoclonal)
InvitrogenCat# 11-0341-82; RRID: AB_465021(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-Flt3 (CD135)-APC
(clone: A2F10, rat monoclonal)
BioLegendCat# 135310; RRID: AB_2107050(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-CD127 (IL-7Rα)
(clone: A7R34, rat monoclonal)
BioLegendCat# 135023; RRID: AB_10897948(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-CD201 (EPCR)-PE (clone: RCR-16, rat monoclonal)BioLegendCat# 141504; RRID: AB_10899579(0.5 µL, 1 µL, or 2 µL/mouse)
AntibodyAnti-Ki67-Alexa Fluor555
(clone: B56, mouse monoclonal)
BD biosciencesCat# 558617(10 µL/sample)
AntibodyAnti-Ki67 Monoclonal Antibody (SolA15), eFluor 660, eBioscience
(Clone: SolA15, mouse monoclonal)
InvitrogenCat# 50-5698-82; RRID: AB_2574235(10 µL/sample)
AntibodyFc-block (anti-mouse CD16/32)
(clone: 2.4-G2, rat monoclonal)
BD biosciencesCat# 553142; RRID: AB_394657(2 µL/mouse)
AntibodyAnti-CD16/CD32 Monoclonal Antibody (93),
Alexa Fluor 700 (clone: 93, rat monoclonal)
InvitrogenCat# 56-0161-82; RRID: AB_493994(2 µL/mouse)
AntibodyPhospho-Rb (Ser807/811) (D20B12) XP (rabbit monoclonal)Cell Signaling TechnologyCat# 8516(1:200)
AntibodyAnti-human CD8-APC (clone: SK1, mouse monoclonal)BiolegendCat# 344721; RRID: AB_2075390(1 µL/sample)
AntibodyRecombinant anti-PFKFB3 antibody (rabbit monoclonal)AbcamCat# ab181861(1:100)
AntibodyAnti-PFK2 (Ser467) antibody (rabbit polyclonal)BiossCat# bs-3331R(1:100)
AntibodyRecombinant anti-methyl-PFKFB3 antibody (rabbit polyclonal)Obtained from
Takehiro Yamamoto at Keio University
DOI: 10.1038/ncomms4480
N/A(1:100)
Gene (Mus musculus)Pfkfb3This paperN/ADetails are as described in Methods
Gene (Mus musculus)Pfkfb3CAThis paperN/ADetails are as described in Methods
Recombinant DNA reagentpMYs-IRES-GFPObtained from
Toshio Kitamura at IMUST
N/AUsed as backbone vector for gene overexpression
Recombinant DNA reagentpMYs-IRES-human CD8Obtained from
Go Nagamatsu at Kyushu University
N/AUsed as backbone vector for gene overexpression
Recombinant DNA reagentPfkfb3-knockout gRNA (s)Custom made in lab or purchased from Synthego, Inc.N/ADetails are as described in Methods
Recombinant DNA reagentRosa-knockout gRNACustom made in labN/ADetails are as described in Methods
Recombinant DNA reagentCD45-knockout gRNACustom made in labN/ADetails are as described in Methods
Chemical compound, drugISTThermo Fisher ScientificCat# 41400–045
Chemical compound, drugPenicilinMeiji SeikaPGLD755
Chemical compound, drugStreptomycin sulfateMeiji SeikaSSDN1013
Chemical compound, drugSodium seleniteNacalai TesqueCat# 11707–04
Chemical compound, drugFetal bovine serumBiowestCat# S1820-500
Chemical compound, drugFetal bovine serumThermo Fisher ScientificCat# 10270–106
Chemical compound, drugBovine serum albuminSigma AldrichCat# A4503-50G/100 G
Chemical compound, drug2-mercapto ethanol (2-ME) 1000 xLife TechnologiesCat# 21985–023
Chemical compound, drugThymidineTokyo Chemical Industry Co., Ltd.Cat# T0233
Chemical compound, drugRPMI 1640 Amino Acids Solution (50×)Sigma AldrichCat# R7131
Chemical compound, drugMEM Vitamin Solution (100×)Sigma AldrichCat# M6895
Chemical compound, drugL-glutamineSigma AldrichCat# G8540
Chemical compound, drugL-alanineSigma AldrichCat# A7469
Chemical compound, drugL-SerineSigma AldrichCat# S4311
Chemical compound, drugD(+)-GlucoseWakoCat# 049–31165
Chemical compound, drug13C-glucoseSigma AldrichCat# 389374
Chemical compound, drug2-NBDGCayman ChemicalCat# 11046
Chemical compound, drugCytochalasin BWakoCat# 030–17551
Chemical compound, drugPhloretinTCI chemicalsCat# P1966
Chemical compound, drug2-morpholinoethanesulfonic acidWakoCat# 341–01622
Chemical compound, drugmethionine sulfoneAlfa AesarCat# A17027
Chemical compound, drugSodium L-lactateSigma AldrichCat# L7022
Chemical compound, drugCholesterol Lipid Concentrate (250 X)GibcoCat# 12531018
Chemical compound, drug100mM-Sodium Pyruvate SolutionNacalai tesqueCat# 06977–34
Chemical compound, drugSodium HydroxideWakoCat# 194–18865
Chemical compound, drug5-fluorouracilKyowa Hakko KirinN/A
Chemical compound, drug2-Deoxy-D-GlucoseTokyo Chemical Industry Co., Ltd.Cat# D0051
Chemical compound, drugOligomycinCell Signaling TechnologyCat# 9996 L
Chemical compound, drugFCCPSigma AldrichCat# C2920
Chemical compound, drugRotenoneSigma AldrichCat# R8875
Chemical compound, drugEtomoxir (sodium salt)Cayman chemicalCat# 11969
Chemical compound, drug6-diazo-5-oxo-L-nor-LeucineCayman chemicalCat# 17580
Chemical compound, drugVerapamilSigma AldrichCat# V4629
Chemical compound, drugN-acetyl-cysteineTokyo Chemical Industry Co., Ltd.Cat# A0905
Chemical compound, drugAZ PFKFB3 26R&D systemsCat# 5675
Chemical compound, drugDorsomorphin dihydrochlorideSanta Cruz BiotechnologyCat# sc-361173
Chemical compound, drugLKB1/AAK1 dual inhibitorChem SceneCat# CS-0342
Chemical compound, drugPKM2 inhibitor(compound 3 k)SelleckCat# S8616
Chemical compound, drugRecombinant Murine SCFPeproTechCat# 250–03
Chemical compound, drugRecombinant Human TPOPeproTechCat# 300–18
Chemical compound, drugα-hemolysinSigma AldrichCat# H9395
Chemical compound, drugPotassium ChlorideWakoCat# 7447-40-7
Chemical compound, drugSodium ChlorideWakoCat# 7647-14-5
Chemical compound, drugCalcium Nitrate TetrahydrateWakoCat# 13477-34-4
Chemical compound, drugMagnesium Sulfate (Anhydrous)WakoCat# 7487-88-9
Chemical compound, drugSodium Hydrogen CarbonateWakoCat# 144-55-8
Chemical compound, drugDisodium Hydrogenphosphate 12-WaterWakoCat# 10039-32-4
Chemical compound, drugGlutathione reduced formTokyo Chemical Industry Co., Ltd.Cat# G0074
Chemical compound, drugEthylene Glycol Bis(β-aminoethylether)-N,N,N',N'-tetraacetic AcidNacalai tesqueCat# 15214–21
Chemical compound, drugHEPESWakoCat# 7365-45-9
Chemical compound, drugMagnesium ChlorideWakoCat# 7786-30-3
Chemical compound, drugAdenosine 5’-triphosphate magnesium saltSigma AldrichCat# A9187
Chemical compound, drugDMSOSigma AldrichCat# D8418
Chemical compound, drugEthanolNacalai tesqueCat# 14712–63
Chemical compound, drugMethanolNacalai tesqueCat# 21914–03
Chemical compound, drugChloroformNacalai tesqueCat# 08401–65
Chemical compound, drugHoechst 33432Thermo Fisher ScientificCat# H3570(10 µg/mL)
Chemical compound, drugPropidium iodideThermo Fisher ScientificCat# P3566(1:1000)
Chemical compound, drugFlow-Check FluorspheresBeckman CoulterCat# 7547053
Chemical compound, drugTrueCut Cas9 Protein v2Thermo Fisher ScientificCat# A36498
Chemical compound, drugExTaqTakara bioCat# RR001
Chemical compound, drugNotINippon GeneCat# 312–01453
Chemical compound, drugEcoRINippon GeneCat# 314–00112
Chemical compound, drugRetroNectin (Recombinant Human Fibronectin Fragment)TakaraCat# T100A
Chemical compound, drugUltraPure DNase_RNase-Free Distilled WaterInvitrogenCat# 10977015
Chemical compound, drugGSK3368715MedChemExpressCat# HY-128717A
Commercial assay or kitRNeasy Mini KitQIAGENCat# 74104
Commercial assay or kitSuperScript VILOThermo Fisher ScientificCat# 11754–050
Commercial assay or kit2-mercapto ethanolSigma AldrichCat# M6250
Commercial assay or kitFlow Cytometry Size Calibration Kit (nonfluorescent microspheres)InvitrogenCat# F13838
Commercial assay or kit‘’Cellno’’ ATP assay reagent Ver.2Toyo B-Net CorporationCA2-50
Commercial assay or kitFixation and Permeabilization SolutionBD BiosciencesCat# 554722
Commercial assay or kitPerm/Wash BufferBD BiosciencesCat# 554723
Commercial assay or kitCellROX Deep Red ReagentInvitrogenCat# C10422
Commercial assay or kitSMART-Seq v4 Ultra Low Input RNA Kit for SequencingClontechCat# Z4888N
Commercial assay or kitNEBNext Ultra DNA Library Prep Kit for IlluminaNew England BioLabsCat# E7370S
Commercial assay or kitCUGA7 gRNA Synthesis KitNippon GeneCat# 314–08691
Commercial assay or kitExtract-N-Amp Blood PCR KitMerckCat# XNAB2-1KT
Commercial assay or kitWizard SV Gel and PCR Clean-Up SystemPromegaCat# A9281
Commercial assay or kitBD Pharmingen FITC BrdU Flow KitBD BiosciencesCat# 559619
Commercial assay or kitBD Pharmingen PE Annexin V Apoptosis Detection Kit IBD BiosciencesCat# 559763
Commercial assay or kitFAOBlueFunakoshiCat# FDV-0033
Software, algorithmR v3.5.2R Development Core Team, 2018http://www.r-project.org
Software, algorithmTopHat v2.0.1310.1186/gb-2013-14-4-r36; Kim et al., 2013https://ccb.jhu.edu/software/tophat/index.shtml
Software, algorithmCufflinks v2.2.110.1038/nbt.1621; Trapnell et al., 2012http://cole-trapnell-lab.github.io/cufflinks/
Software, algorithmGSEA software v4.3.0Broad Institute; Subramanian et al., 2005https://www.gsea-msigdb.org/gsea/index.jsp
Software, algorithmFlowJo version 9BD Bioscienceshttps://www.flowjo.com/
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Additional files

Supplementary file 1

Custom RPMI medium for culture and ATP analysis.

Composition of custom RPMI medium for culture (upper) and ATP analysis (lower). “-“ means 0 mg/L.

https://cdn.elifesciences.org/articles/87674/elife-87674-supp1-v1.xlsx
Supplementary file 2

In vitro tracer analysis for 5-FU-treated HSCs.

Results of tracer analysis using U-13C6-glucose with HSCs from mice treated with PBS or 5-FU. Each section contains raw data from the glycolytic system, TCA cycle, and P~NAS from top to bottom. Data from three individual experiments are described for each. All values represent average metabolite levels in single HSCs obtained by dividing the metabolite levels detected in HSCs (compared to internal standards) by the number of HSCs used in the analysis.

https://cdn.elifesciences.org/articles/87674/elife-87674-supp2-v1.xlsx
Supplementary file 3

In vitro tracer analysis for oligomycin-treated HSCs.

Results of tracer analysis using U-13C6-glucose with HSCs treated with DMSO (Oligomycin-) or oligomycin (Oligomycin+). Each section contains raw data from the glycolytic system, TCA cycle, and P~NAS from top to bottom. Data from four individual experiments are described for each. All values represent average metabolite levels in single HSCs, obtained by dividing the metabolite levels detected in HSCs (compared to internal standards) by the number of HSCs used in the analysis.

https://cdn.elifesciences.org/articles/87674/elife-87674-supp3-v1.xlsx
Supplementary file 4

13C quantitative metabolic flux analysis.

Metabolic flux values of each enzyme obtained from 100 trials of 13C quantitative metabolic flux analysis for PBS-treated (left), 5-FU-treated (middle), and OXPHOS-inhibited HSCs (right).

https://cdn.elifesciences.org/articles/87674/elife-87674-supp4-v1.xlsx
Supplementary file 5

In vivo tracer analysis for 5-FU treated mice.

Results of tracer analysis during continuous in vivo administration of U-13C6-glucose to mice treated with 5-FU or PBS. A sheet is prepared for each metabolite and each contains two tables. The A.U. table (left) shows the metabolite levels detected in the four biological replicates in the 5-FU and PBS groups, obtained by dividing the metabolite levels detected in HSCs (compared to internal standards) by the number of HSCs used in the analysis. The ratio table (right) shows the calculated percentage of labeled metabolites among detected metabolites, where 12 C indicates unlabeled metabolites and 13Cn indicates n-carbon labeled metabolites by U-13C6-glucose.

https://cdn.elifesciences.org/articles/87674/elife-87674-supp5-v1.xlsx
Supplementary file 6

Primer list for genotyping PCR.

https://cdn.elifesciences.org/articles/87674/elife-87674-supp6-v1.xlsx
MDAR checklist
https://cdn.elifesciences.org/articles/87674/elife-87674-mdarchecklist1-v1.docx

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  1. Shintaro Watanuki
  2. Hiroshi Kobayashi
  3. Yuki Sugiura
  4. Masamichi Yamamoto
  5. Daiki Karigane
  6. Kohei Shiroshita
  7. Yuriko Sorimachi
  8. Shinya Fujita
  9. Takayuki Morikawa
  10. Shuhei Koide
  11. Motohiko Oshima
  12. Akira Nishiyama
  13. Koichi Murakami
  14. Miho Haraguchi
  15. Shinpei Tamaki
  16. Takehiro Yamamoto
  17. Tomohiro Yabushita
  18. Yosuke Tanaka
  19. Go Nagamatsu
  20. Hiroaki Honda
  21. Shinichiro Okamoto
  22. Nobuhito Goda
  23. Tomohiko Tamura
  24. Ayako Nakamura-Ishizu
  25. Makoto Suematsu
  26. Atsushi Iwama
  27. Toshio Suda
  28. Keiyo Takubo
(2024)
Context-dependent modification of PFKFB3 in hematopoietic stem cells promotes anaerobic glycolysis and ensures stress hematopoiesis
eLife 12:RP87674.
https://doi.org/10.7554/eLife.87674.3