Supplemental Figure S1. RANK expression on human lung cancer cells.

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Supplemental Figure S1. RANK expression on human lung cancer cells. (A) Incidence and H-Scores of RANK expression determined from IHC in the indicated primary lung cancer subgroups. The overall expression was generated using the H-scoring method which is the sum of the products of percentage of cells multiplied the intensity (0-3). Incidence was scored as the percent of tumors that showed any positive IHC signal. () Representative flow cytometry to detect RANK cell surface expression on EpCAM H1299 cells that do not express RANK, EpCAM + PC3 cells as RANK expressing positive control cells, and an EpCAM + resected primary NSCLC adenocarcinoma. Isotype control stainings are shown in the left panels. (C) Positive correlation between RANK flow cytometry results and IHC analysis on a subset of disaggregated primary human lung tumors (n=33). To confirm RANK flow cytometry results and to better understand the distribution of RANK expression, IHC was performed using a validated internal RANK IHC assay. H-Scores ranged from 0 to 260. (D) Representative images of RANK expression in a primary dissected NSCLC adenocarcinoma and a squamous lung tumor, using samples from a second lung cancer cohort (Graz cohort). Scale bars, 50μm and in insets, 20μm. (E) Detection of TRAP levels in the serum of PS or OPG-Fc [10mg/kg] treated PDX mice assessed at study termination. TRAP levels indicate osteoclast activity. Data for individual mice are shown. Statistical comparisons were performed using Chi-square test. Supplemental Figure S2. Deletion of RANK has no apparent effect on lung structures or lung function. (A) Immunofluorescence staining to detect RANK protein expression in normal lung tissue. Note RANK protein (green) is primarily expressed in bronchial epithelial cells. DAPI (blue) was used 1

to counterstain for nuclei. Scale bars, 100µm. () Representative histological images of lung tissues isolated from SP-C Cre;KRas;rank +/+ and SP-C Cre;KRas;rank f/f mice. Scale bars, upper panels, 2mm; lower panels 500 m. (C) qpcr analysis of RANK mrna levels in primary pneumocytes purified from SP-C Cre; KRas;rank +/+ and SP-C Cre;KRas;rank f/f mice. ***p<0.001 (Unpaired, two-sided t-test). (D) Comparison of average O2 consumption and CO2 production between SP-C Cre;KRas;rank +/+ and SP-C Cre;KRas;rank f/f mice using the PhenoMaster module for indirect gas calorimetry. No significant differences were detected in O2 consumption and CO2 production; as a consequence the respiratory exchange rate (RQ) was also comparable between SP-C Cre;KRas;rank +/+ and SP-C Cre;KRas;rank f/f mice. (E) Immunofluorescence staining to detect RANK protein expression (green) in lung tumors from KRas;rank +/+ and KRas;rank fl/fl littermate mice 28 weeks after AdCre injections. Asterix indicates RANK expression in KRas;rank +/+ tumor tissue. Note RANK expression in the bronchial epithelium (arrow) adjacent to the RANK deficient lung tumor in the KRas;rank fl/fl mouse. DAPI (blue) was used to counterstain for nuclei. Scale bars, 100 m. Supplemental Figure S3. Epithelial deletion of RANK but not RANKL controls Kras G12D -driven lung tumorigenesis. (A) Representative 3D microct movies of lung tumors of KRas;rank +/+ and KRas;rank fl/fl littermate mice assayed 25 weeks after AdCre inhalation. The movies have been separately deposited, please click the links. () Kaplan Meier survival curves for KRas;rankl +/+ (n=26, median survival=205 days) and KRas;rankl fl/fl (n=17, median survival=231 days) littermate mice injected intranasally with AdCre (2.5 10 7 PFU). There was no statistically significant difference 2

between the two cohorts (log rank test). (C) Representative histological images of lung tumors in KRas;rankl +/+ and KRas;rank fl/fl mice, 6 and 30 weeks after AdCre inhalation. Scale bars, 2mm. Supplemental Figure S4. Deletion of RANK has no apparent effect on intratumoral immune cells populations. Comparative immunoprofiling of the early lung lesions from both KRas;rank +/+ and KRas;rank fl/fl mice using flow cytometry 6 weeks after Ad-Cre inhalation. No significant difference was observed in in the assessed populations of T cells and NK cells (A), Foxp3 + regulatory T cells (), 220 + cells (C), inflammatory T cells (D) and different myeloid cell subsets (E). Supplemental Figure S5. Gene expression profiling of KRas;rank +/+ and KRas;rank fl/fl pneumocytes. (A) qpcr analysis to control for RANK mrna expression in primary pneumocytes isolated from KRas;rank +/+ and KRas;rank fl/fl mice. Purified pneumocytes were infected with AdCre to induce mutant KRas and to delete RANK in cells with rank fl/fl alleles. Relative expression levels (+/- SEM) are shown as compared to RANK expressing KRas;rank +/+ control cells (values set to 1). ( and C) Gene sets enriched in primary KRas;rank +/+ and KRas;rank fl/fl pneumocytes using GSEA (normalized enrichment score (NES). Left, GSEA enrichment plot of the enrichment score (ES; y- axis) reflecting the degree of the gene sets overrepresentation in KRas;rank +/+ and KRas;rank fl/fl pneumocytes at the extreme left or right of the entire ranked list. Solid bars represent genes of the 3

gene set. Right, GSEA-derived heatmap illustrating gene expression profiles of the leading edge subset. () Examples of gene sets over-represented in KRas;rank fl/fl pneumocytes (cell adhesion) or overrepresented in control KRas;rank +/+ pneumocytes (mitosis). (C) Examples of enrichment for mitochondrial structure and mitochondrial respiration genes in KRas;rank +/+ as compared to KRas;rank fl/fl pneumocytes. Supplemental Figure S6. RANKL/RANK couple to mitochondrial respiration in primary pneumocytes and murine and human lung cancer cells. (A) ATP production, basal respiration, maximal respiration and spare respiratory capacity (mean values +/- SEM) based on bioenergetics Seahorse profiling of purified primary pneumocytes from KRas;rank +/+ and KRas;rank fl/fl mice. Purified pneumocytes were infected with AdCre to induce mutant KRas and to delete RANK in cells with rank fl/fl alleles; these KRas;rank +/+ and KRas;rank fl/fl cells were then treated with RANKL [1 g/ml] for 24 hours and as controls left without RANKL treatment. A minimum of 5 replicates were analyzed for each condition and pneumocytes purified from 3 different mice were used independently. *p<0.05, **p<0.01 (Unpaired, two-sided t-test). () ATP production, basal respiration, maximal respiration, and spare respiratory capacity (mean values +/- SEM) based on bioenergetics profiling of purified primary lung tumor cells from KRas;rank +/+ and KRas;rank fl/fl mice 18 weeks after in vivo AdCre inhalation. A minimum of 5 replicates (OCR +/- SEM) were analyzed for each condition and purified primary lung tumor cells from 3 different mice were used independently. See also Extended Fig. 3d. ***p<0.001 (Unpaired, two-sided t-test). (C) qrt-pcr analysis to determine RANK mrna expression in the indicated human lung cancer cell lines. Relative RANK mrna 4

expression levels (+/- SEM, n = 3) are shown as compared to human peripheral blood mononuclear cells (value arbitrarily set at 1). (D) ioenergetics OCR profiling of ATP production, basal respiration, maximal respiration and spare respiratory capacity based on bioenergetics Seahorse profiling of the indicated human lung cancer cell lines. Cells were stimulated with RANKL [1 g/ml] for 2 hours (red lines and bars) and as controls left without RANKL treatment (black lines and bars). Data are all shown as mean values +/- SEM. A minimum of 6 replicates were analyzed for each condition and lung cancer cell line; experiments were independently repeated 3 times. *p<0.05, **p<0.01 (Unpaired, two-sided t-test). Supplemental Figure S7. RANKL/RANK triggers lung cancer stem-like cells proliferation and mitochondrial homeostasis. (A) Western blotting of A427 human lung cancer cells to determine activation of the indicated signaling pathway in response to RANKL stimulation [1 g/ml]. Activation was determined at the indicated time points using phospho-specific Abs to detect p65 NF-, AKT and p38-mapk. The respective total proteins are shown to control for protein expression. -actin is shown as a loading control. () Western blot analysis of purified KRas;rank +/+ and KRas;rank fl/fl tumor cells to determine activation of the PGC1 in response to RANKL (1 g/ml) stimulation, analysed at indicated time points. -actin is shown as a loading control. (C) Determination of PGC1 protein expression in purified KRas;rank +/+ and KRas;rank fl/fl tumor cells stimulated with RANKL or RANKL plus inhibitors of AKT, P38 and NF-, respectively. (D) 3D tumor spheroids assay of purified KRas;rank +/+ tumor cells treated with RANKL or RANKL plus inhibitors of AKT, P38 5

and NF-, respectively. 5000 primary tumor cells were seeded. Experiments were performed with 6 replicates for each condition and repeated with 3 different KRas;rank +/+ mice. Scale bars, 1mm. (E) Quantification (mean values +/- SEM) of tumor spheroids numbers as shown in the representative images in (D). **p<0.01, ***p<0.001 (Unpaired, two-sided t-test). Supplemental Figure S8. RANKL stimulation does not induce enhanced tumor sphere formation in KRas;rank fl/fl mutant tumor cells. (A) 3D tumor spheroids assay of purified KRas;rank fl/fl tumor cells treated with RANKL [1 g/ml] or oligomycin alone [low dose is 0.05 g/ml, high dose is 0.5 g/ml] or RANKL plus different oligomycin concentrations. 5000 primary tumor cells were seeded. Experiments were performed with 6 replicates for each condition and repeated with 3 different KRas;rank fl/fl mice. Scale bars, 1mm. () Quantifications (mean +/- SEM) of tumor spheroids numbers of (A) N.S, not significant (Unpaired, two-sided t-test). (C) Representative images for rdu staining of tumor spheroids derived from KRas;rank fl/fl primary lung tumor cells, which received no treatment, or were treated with RANKL alone [1 g/ml], oligomycin alone [low dose is 0.05 g/ml, high dose is 0.5 g/ml] and RANKL plus different oligomycin concentrations. 5000 primary tumor cells were seeded. rdu labelling [10 M/ml] was performed for 2 hours. Experiments were performed with 6 replicates for each condition and repeated with 3 different KRas;rank fl/fl mice. Sections were counter-stained with DAPI. (D) Quantifications (mean +/- SEM) rdu + cells within tumor spheroids as shown in (C). N.S, not significant (Unpaired, two-sided t-test). Scale bars, 50 m. 6

Supplemental Figure S9. RANKL, RANK, and OPG expression in human lung cancer. (A) Prediction of overall survival probability in males versus females in the human Affymetrix lung adenocarcinoma dataset stratified for high (red lines) and low (black lines) RANK, RANKL, and OPG mrna expression based on the best fit algorithm for. Data presented were obtained using KM plotter. P values (log rank test) and total numbers of patients with either low (black lines) or high (red lines) RANK, RANKL and OPG expression, respectively, are indicated. () Cross-correlation matrixes to compare RANKL and RANK protein expression (determined by IHC) on human lung tumors with gender. n = 364, Uppsala cohort with early stage treatmentnaïve resected lung cancer, including SCC, AC, SCLC and LCC. P values are indicated, calculated using the Fisher s Exact test. Supplemental Table S1. Significantly enriched c5/go gene sets (FDR <0.1) from a GSEA analysis of KRas;rank fl/fl versus KRas;rank +/+ pneumocytes. 7

A Non-small Cell Lung Cancer Adenocarcinoma Squamous Cell Carcinoma Rao_Supplemental Fig S1 Small Cell Carcinoma RANK # of samples % positive Mean H-score # of samples % positive Mean H-score # of samples % positive Mean H-score 58 72 60 62 61 20 29 65 63 H1299 negative control C RANK IHCHScore 300 200 100 E TRAP U/L P<0.0001 Cell counts Isotype RANK PC3 positive control RANK + human lung tumor D 0 0.8 1.0 1.2 1.4 1.6 1.8 RANK Flow Cytometry Measurement (Fold Change Over Isotype) RANK - IHC Adenocarcinoma Squamous tumor

Rao_Supplemental Fig S2 A Control RANK C D 1.4 4000 3000 2000 1000 average O2 consumption [ml/h/kg] 0 SP-C Cre;KRas;rank +/+ SP-C Cre;KRas;rank f/f 4000 3000 2000 1000 average CO2 production [ml/h/kg] 1.2 1 0.8 0.6 0.4 0.2 0 *** 0 SP-C Cre;rank +/+ SP-C Cre;rank f/f E RANK - IF KRas;rank fl/fl KRas;rank +/+ Relative RANK mrna expression

A KRas;rank +/+ Rao_Supplemental Fig S3 KRas;rankl +/+ n=26 KRas;rankl fl/fl n=17 Percent survival KRas;rank fl/fl C Days post AdCre inhalation KRas;rankl +/+ 24.15% KRas;rankl f/f 4.93% 6 weeks after AdCre inhalation 30 weeks after AdCre inhalation

A T cells and NK cells C D E Rao_Supplemental Fig S4 KRas;rank +/+ KRas;rank fl/fl %CD45 + 220 + cells %CD45 + cells %CD45 + cells %Foxp3 + of CD4 + T cells

A KRas;rank +/+ C Rao_Supplemental Fig S5 KRas;rank fl/fl

A KRas;rank +/+ pneumocytes ** * * Control RANKL C Rao_Supplemental Fig S6 Human lung cancer cells KRas;rank fl/fl pneumocytes ATP production ATP production asal respiration Murine primary lung cancer cells asal respiration *** *** Maximum respiration KRas;rank +/+ KRas;rank fl/fl Spare respiratory capacity D A427 H1437 OCR(pmol/min) OCR(pmol/min) Human lung cancer cells ** ** ** ** * Control RANKL Spare respiratory capacity *** Max. respiration *** H2122 H460 OCR(pmol/min) OCR(pmol/min) ATP production asal respiration Max. respiration Spare Respiratory capacity

A RANKL P-p65 NF-k p65 NF-k P-AKT AKT P-p38 p38 A427 0 15 30 min C KRas;rank +/+ KRas;rank fl/fl w/o +RANKL iakt ip38 inf- PGC1- actin PGC1- actin E # Tumor spheres Rao_Supplemental Fig S7 ** 100 ** *** 80 60 40 20 0 -actin RANKL D Control RANKL RANKL w/o 1h 12h 24h KRas;rank +/+ PGC1- actin RANKL+iAKT RANKL+iP38 RANKL+iNF- KRas;rank fl/fl PGC1- actin

Rao_Supplemental Fig S8 A Control Oligomycin (0.5 g/ml) Oligomycin (0.05 g/ml) C Control Oligomycin (0.5 g/ml) Oligomycin (0.05 g/ml) RANKL Control RANKL Control # tumor spheres 50 40 30 20 10 N.S KRas;rank fl/fl N.S N.S D % rdu + cells 10% 8% 6% 4% 2% N.S KRas;rank fl/fl N.S N.S 0 RANKL + + + high high low low Oligomycin 0% RANKL + + + high high low low Oligomycin

A RANK females RANK males Rao_Supplemental Fig S9 Gender Survival probability p=0.16 n = 715 p=0.1 n = 1100 Male Female RANK 113 (60.4 %) 92 (56.1%) RANK+ 74 (39.6 %) 72 (43.9 %) Male Female Time (month) Time (month) RANKL 87 (46.5 %) 55 (33.5 %) RANKL+ 100 (53.5 %) 109 (66.5 %) Survival probability RANKL females p=0.0098 n = 715 RANKL - males p=0.038 n = 1100 Fisher s exact test: p = 0.448 for RANK and gender and p = 0.01641 for RANKL and females. Time (month) Time (month) OPG females OPG males Survival probability p=1.4e 06 n = 715 p=0.0059 n = 1100 Time (month) Time (month)

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