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Supplementary Figure 1. FGFR1-4 DNA CN, mRNA levels and ROC curves analysis. A) Waterfall plot representing the best antitumor response of FGFRi in 24 patients from 8 different cancer types treated at VHIO. FGFR1/2 amplification status and high FGFR1-4 mRNA levels are indicated in the underneath panel. B) Copy number (CN) values of FGFR1-4 by MSK-IMPACT in the FGFR/FGFamp PDX collection and categorized analysis in PDXs harboring CN amplification (CN>4), according to the response to rogaratinib (responders (SD and PR) and non-responders (PD)). C) Evaluation of FGFR1/4 CN ratio by FISH ratio (the dashed line indicates the CN ratio>2.2 that is considered amplified) and categorized analysis according to the response to rogaratinib. D) Correlation analysis between the CN values (X-axis) and mRNA levels (Y-axis) of FGFR1-4 obtained from MSK-IMPACT or nCounter, respectively. Pearson correlation coefficient (r2) is shown. E) Categorized analysis of FGFR1-4 mRNA composite biomarker according to the response to rogaratinib, obtained from HTG or qPCR data. Statistical test: Mann-Whitney U test. ROC curve analysis the FGFR1-4 mRNA composite biomarker, obtained from HTG or qPCR (AUC=0.89, both).

Purpose:FGFR1 amplification (FGFR1amp) is recurrent in metastatic breast cancer (MBC) and is associated with resistance to endocrine therapy and CDK4/6 inhibitors (CDK4/6is). Multi-tyrosine kinase inhibitors (MTKIs) and selective pan-FGFR inhibitors (FGFRis) are being developed for FGFR1amp breast cancer. High-level FGFR amplification and protein expression by IHC have identified breast cancer responders to FGFRis or MTKIs, respectively.Experimental Design:Here, we used preclinical models and patient samples to identify predictive biomarkers to these drugs. We evaluated the antitumor activity of an FGFRi and an MTKI in a collection of 17 breast cancer patient–derived xenografts (PDXs) harboring amplification in FGFR1/2/3/4 and in 10 patients receiving either an FGFRi/MTKI. mRNA levels were measured on FFPE tumor samples using two commercial strategies. Proliferation and angiogenesis were evaluated by detecting Ki-67 and CD31 in viable areas by immunofluorescence.Results:High FGFR1–4 mRNA levels but not copy-number alteration (CNA) is associated with FGFRi response. Treatment with MTKIs showed higher response rates than with FGFRis (86% vs. 53%), regardless of the FGFR1–4 mRNA levels. FGFR-addicted PDXs exhibited an antiproliferative response to either FGFRis or MTKIs, and PDXs exclusively sensitive to MTKI exhibited an additional antiangiogenic response. Consistently, the clinical benefit of MTKIs was not associated with high FGFR1–4 mRNA levels and was observed in patients previously treated with antiangiogenic drugs.Conclusions:Tailored therapy with FGFRis in molecularly selected MBC based on high FGFR1–4 mRNA levels warrants prospective validation in patients with CDK4/6i-resistant luminal breast cancer and in patients with TNBC without targeted therapeutic options.

Supplementary Table S2 HTG OBP panel raw data

Supplementary Figure Legends

Here, we used preclinical models and patient samples to identify predictive biomarkers to these drugs. We evaluated the antitumor activity of an FGFRi and an MTKI in a collection of 17 breast cancer patient-derived xenografts (PDXs) harboring amplification inHighTailored therapy with FGFRis in molecularly selected MBC based on high

CDK4/6 inhibitors combined with endocrine therapy have demonstrated higher antitumor activity than endocrine therapy alone for the treatment of advanced estrogen receptor-positive breast cancer. Some of these tumors are de novo resistant to CDK4/6 inhibitors and others develop acquired resistance. Here, we show that p16 overexpression is associated with reduced antitumor activity of CDK4/6 inhibitors in patient-derived xenografts (n = 37) and estrogen receptor-positive breast cancer cell lines, as well as reduced response of early and advanced breast cancer patients to CDK4/6 inhibitors (n = 89). We also identified heterozygous RB1 loss as biomarker of acquired resistance and poor clinical outcome. Combination of the CDK4/6 inhibitor ribociclib with the PI3K inhibitor alpelisib showed antitumor activity in estrogen receptor-positive non-basal-like breast cancer patient-derived xenografts, independently of PIK3CA, ESR1 or RB1 mutation, also in drug de-escalation experiments or omitting endocrine therapy. Our results offer insights into predicting primary/acquired resistance to CDK4/6 inhibitors and post-progression therapeutic strategies.