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Additional file 6: Figure S6. A. Relative number of living (relative survival) SKBR3 RANK cells stimulated with RANKL in the presence or absence of denosumab (DNS) and incubated for 4 days with the indicated concentrations of lapatinib. Cells were seeded in growth media with/without denosumab (1 μg/ml), lapatinib was added after 24 h stimulation with 100 ng/ml RANKL, and cell viability was analyzed with CCK8 as detailed in methods. Determinations were done in triplicates, mean values from n ≥ 2 independent experiments and SD are depicted. B. Western blot analyses of total levels of p65, ERK1/2 and HER2 in whole lysates from SKBR3, BT474 and HCC1954 cells stably transduced with control (empty) or RANK overexpressing (RANK) vectors as depicted in Fig. 5d. Before collecting the cells, they were cultured in media without FBS for 12 h, pretreated with/without lapatinib for 2 h followed by 10 min stimulation with RANKL. Tubulin was used as a loading control. C. Table depicting the relative phospho-protein levels of the indicated proteins from the western blots shown in Fig. 5d and Fig. S6B determined by densitometry analyses with Image J.

Additional file 3: Figure S3. RANK and RANKL expression in breast cancer samples from the PAMELA clinical trial. A. Expression of RANK and RANKL across the intrinsic molecular subtypes from the PAMELA study. P values were calculated by comparing mean values across all groups. B. Scatter plots of RANK and RANKL expression versus ERBB2 expression for baseline samples in the PAMELA study. Solid line in each figure represents the regression line. Pearson correlation coefficient (r) with significance (p value) is presented in each figure. C. Pearson correlation between single genes and gene expression signatures evaluated in baseline samples from the PAMELA study.

Additional file 5: Figure S5. A. Relative number of living (relative survival) SKBR3 and SKLR control cells incubated for 4 days with the indicated concentrations of lapatinib and stimulated with RANKL. Cells were seeded in growth media, 100 ng/ml RANKL were added 24h after seeding, lapatinib was added 24 h later and cells were analyzed with CCK8 as detailed in methods. Determinations were done in triplicates, mean values are depicted from n = 5 independent experiments and SD and p-value (**) calculated by one-way ANOVA is depicted (p ≤ 0.05 for SKBR3 vs SKLR and SKLR +RANKL, SKBR3 +RANKL vs SKLR and SKLR +RANKL; n.s. for SKBR3 vs SKBR3 +RANKL and SKLR vs SKLR +RANKL). Significance of relative survival was calculated for each concentration using two-tailed p values for one sample t test. RANKL significantly increased survival of SKLR cells at 0.018 μM of lapatinib (p = 0.019). B. Western blot showing the total levels of IκB, p65, ERK1/2, AKT and HER2 in SKBR3 control, SKLR control and SKLR sh#3 cells treated with RANKL or lapatinib as depicted in Fig. 4c. Cells were serum starved for 12 h and then treated with lapatinib (2 h) or RANKL (10 min) before processing them. Tubulin was used as a loading control. C. Table depicting the relative phospho-protein levels of the indicated proteins from the western blots shown in Fig. 4c and Fig. S5B determined by densitometry analyses with Image J.

Additional file 7: Figure S7. Western blot analyses of HER2 (p-HER2, p-ERK1/2) and NF-κB (p-p65) pathway activation in SKBR3, BT474 and HCC1954 cells stably transduced with empty or RANK overexpressing (RANK) vectors. Cells were cultured in media without FBS for 12 h, followed by stimulation with EGF (100 ng/ml) (upper panels) or heregulin (HRG 10 ng/ml) (lower panels) for the indicated times. Tubulin was used as a loading control.

Additional file 4: Figure S4. RANK but not RANKL expression increased after dual anti-HER2 therapy in HR+ and HR- patient samples (n = 151) from the PAMELA trial. A and B. Ladder plots (left panels) showing RANK and RANKL gene expression in PAMELA HER2-positive HR+ (A) and HR- (B) tumors before (baseline) and after (surgery) dual anti-HER2 treatment. An increase in gene expression is represented in red and a decrease in blue. Each line represents a tumor sample from one patient. P values in A were calculated by comparing mean values between both groups and in B were determined by paired two-tailed t-tests. Density plots (right panels) showing RANK and RANKL gene expression in PAMELA HER2-positive HR+ (A) and HR- (B) tumors before (baseline) and after (surgery) treatment.

Additional file 2: Figure S2. RANK and RANKL staining in TMAs. A. Pictures of RANK and RANKL protein expression analyzed by IHC in the TMA cores from the treatment-naïve cohort. B. Pictures of RANK and RANKL protein expression analyzed by IHC in the TMA cores from the anti-HER2 resistant cohort.

Additional file 2: Figure S2. RANK and RANKL staining in TMAs. A. Pictures of RANK and RANKL protein expression analyzed by IHC in the TMA cores from the treatment-naïve cohort. B. Pictures of RANK and RANKL protein expression analyzed by IHC in the TMA cores from the anti-HER2 resistant cohort.

Additional file 4: Figure S4. RANK but not RANKL expression increased after dual anti-HER2 therapy in HR+ and HR- patient samples (n = 151) from the PAMELA trial. A and B. Ladder plots (left panels) showing RANK and RANKL gene expression in PAMELA HER2-positive HR+ (A) and HR- (B) tumors before (baseline) and after (surgery) dual anti-HER2 treatment. An increase in gene expression is represented in red and a decrease in blue. Each line represents a tumor sample from one patient. P values in A were calculated by comparing mean values between both groups and in B were determined by paired two-tailed t-tests. Density plots (right panels) showing RANK and RANKL gene expression in PAMELA HER2-positive HR+ (A) and HR- (B) tumors before (baseline) and after (surgery) treatment.

Additional file 1: Figure S1. TMA H-scores and controls. A. RANK and RANKL H-scores in HER2-positive breast cancer samples, treatment-naïve (left panels) or anti-HER2-resistant (right panels). In treatment-naïve TMAs, each number represents a “core” from a single patient. In anti-HER2-resistant TMAs, scored independent tumor cores are numbered for each patient (after the symbol #). B. Representative pictures of human breast tumors from patient-derived xenografts used as positive and negative controls for RANK and RANKL IHC.

Additional file 1: Figure S1. TMA H-scores and controls. A. RANK and RANKL H-scores in HER2-positive breast cancer samples, treatment-naïve (left panels) or anti-HER2-resistant (right panels). In treatment-naïve TMAs, each number represents a “core” from a single patient. In anti-HER2-resistant TMAs, scored independent tumor cores are numbered for each patient (after the symbol #). B. Representative pictures of human breast tumors from patient-derived xenografts used as positive and negative controls for RANK and RANKL IHC.