Fig 2: PHGDH regulates nucleotide synthesis in chondrocytes. a Purine (AMP, GMP), pyrimidine (UMP) and ribose-5-phosphate (R-5-P) levels in cultured chondrocytes derived from wild-type (Phgdhchon+) and chondrocyte-specific PHGDH knockout (Phgdhchon-) mice (n = 3). Schematic of carbon atom (circles) transitions of 13C6-glucose used to detect label incorporation into AMP (b) and UMP (c). Serine (Ser; d) and glycine (Gly; e) labeling from 13C6-glucose in cultured chondrocytes (n = 3). Specific mass distribution vectors (MDVs) for each metabolite are shown. f Intracellular Ser and Gly levels in cultured chondrocytes (n = 3). AMP (g), ribose-5-phosphate (R-5-P; h), UMP (i) and aspartate (Asp; j) labeling from 13C6-glucose in cultured chondrocytes (n = 3). Specific MDVs for each metabolite are shown. k Proliferation of cultured chondrocytes with or without nucleotide (nucl) supplementation (n = 4–5), as determined by BrdU incorporation. The data are presented as the means ± SDs; *P < 0.05 vs. Phgdhchon+, **P < 0.01 vs. Phgdhchon+, ***P < 0.001 vs. Phgdhchon+ (Student’s t test), #P < 0.05 (ANOVA)

Fig 3: Clinical implications of RBM15 target genes and clinical efficacy of RBM15 in BC patients.a Molecular subtypes of PHGDH, PSAT1, PSPH, and SHMT2 in the TCGA-BRCA cohort. b Correlations between RBM15 and PHGDH, PSAT1, PSPH, and SHMT2 gene expression in the indicated TCGA-BRCA cohort. Scatter plots of RBM15 and related genes in the cohorts are shown for the indicated cohorts. c, d Kaplan‒Meier plots of OS outcomes in patients from the TCGA-BRCA cohort. e ROC curve analysis was performed to assess the correlation of RBM15 gene expression levels with chemotherapy response by determining the area under the curve (AUC), which was estimated through the concordance index. The corresponding p values were determined using one-sided Wilcoxon’s signed-rank test. f–h After MDA-MB-231 cells were injected into nude mice, the indicated siRNAs containing CH-NPs were administered according to the indicated treatment schedule (f). A representative image of a tumor is shown. g The tumor volumes were measured (h). i Schematic diagram of the RBM15 gene regulatory mechanism. All results are expressed as the means ± standard deviations of three independent replicates (*p < 0.05 and **p < 0.01).

Fig 4: Augmented expression of p21 and MDM2 during serine and glycine (SG)-deprivation promotes adaptation in R248W cells independently of MDM2-facilitated SSP induction. a Growth of the indicated cell lines treated with non-targeting control or p21 siRNA and cultured in SG-depleted medium for 7 days. iRFP intensity in each well on day 7 (top) and iRFP level per well relative to the day 2 reading (bottom) shown for each cell line. Data are represented as the mean of triplicate wells ± SEM for each condition. b Growth of the indicated cell lines treated with non-targeting control or MDM2 siRNA and cultured in SG-depleted medium for 7 days as in (a). c Western blot PSAT-1 and PSPH in the indicated cell lines cultured in SG-depleted medium for 1 or 2 days. Note: this is a re-probe of the blot shown in Fig. 1f, where MDM2 and p21 levels are shown. The ACTIN loading control blot is therefore the same in both figures. d Western blot for SSP enzymes PSAT-1, PSPH and PHGDH, and MDM2 in the indicated cell lines treated with non-targeting control or MDM2 siRNA and grown in SG-depleted medium for 2 days. e Western blot for HA-MDM2 in p53 KO cells transfected with an HA-tagged MDM2 expression construct (HA-MDM2) or a control vector containing GFP. f Growth of p53 KO cells expressing HA-tagged MDM2 or a control vector (EV) and cultured in SG-depleted medium for 9 days. Data are presented as mean ± SEM and depicted as iRFP intensity relative to the initial measurement obtained from triplicate wells per condition.

Fig 5: Histone demethylation regulates osteoclast differentiation.a Schematic overview of experimental setup. Osteoclasts were treated with the JMJD3 inhibitor GSK-J4 during the entire experiment. b, c TRAP staining (b) and quantification of TRAP+ MNCs (c) from wild-type mice treated with either vehicle or GSK-J4 (n = 4; unpaired, two-tailed Student’s t-test). d Phgdh, Csf1r, Tnfrsf11a (encoding for RANK), Nfatc1 (P = 0.007), cMyc, Calcr (P = 0.015), Acp5 (P = 0.007), Ctsk (P = 0.008), Dcstamp (P = 0.02), Atp6v0d2 (P = 0.04), Mmp9 (P < 0.0001) and Irf8 mRNA levels in osteoclasts treated with either vehicle or GSK-J4 (n = 4; unpaired, two-tailed Student’s t-test with *p < 0.05 vs vehicle). e Schematic overview of experimental setup. Osteoclasts were treated with ascorbate during early osteoclast differentiation (that is from d0 to d3). f-g TRAP staining (f) and quantification of TRAP+ MNCs (g) from Phgdhoc+ and Phgdhoc- mice treated with vehicle or ascorbate (n = 4; two-way ANOVA). Scale bar is 50 µm. Data are means ± s.d. Source dat