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Supplementary Table 3. Z-scores of significantly differential expressed genes (provided separately due to size)

Supplementary Table 2. Differential Gene Expression Analysis on BRAF (fusion) gene expressing organoid lines (provided separately due to size)

Fusion genes can be oncogenic drivers in a variety of cancer types and represent potential targets for targeted therapy. The BRAF gene is frequently involved in oncogenic gene fusions, with fusion frequencies of 0.2%–3% throughout different cancers. However, BRAF fusions rarely occur in the same gene configuration, potentially challenging personalized therapy design. In particular, the impact of the wide variety of fusion partners on the oncogenic role of BRAF during tumor growth and drug response is unknown. Here, we used patient-derived colorectal cancer organoids to functionally characterize and cross-compare BRAF fusions containing various partner genes (AGAP3, DLG1, and TRIM24) with respect to cellular behavior, downstream signaling activation, and response to targeted therapies. We demonstrate that 5′ fusion partners mainly promote canonical oncogenic BRAF activity by replacing the auto-inhibitory N-terminal region. In addition, the 5′ partner of BRAF fusions influences their subcellular localization and intracellular signaling capacity, revealing distinct subsets of affected signaling pathways and altered gene expression. Presence of the different BRAF fusions resulted in varying sensitivities to combinatorial inhibition of MEK and the EGF receptor family. However, all BRAF fusions conveyed resistance to targeted monotherapy against the EGF receptor family, suggesting that BRAF fusions should be screened alongside other MAPK pathway alterations to identify patients with metastatic colorectal cancer to exclude from anti-EGFR–targeted treatment.Implications:Although intracellular signaling and sensitivity to targeted therapies of BRAF fusion genes are influenced by their 5′ fusion partner, we show that all investigated BRAF fusions confer resistance to clinically relevant EGFR inhibition.

Supplementary Figure Legends

Supplementary Table 1. KSEA kinase scores and kinase-substrate links identified in phosphoproteomic screen (provided separately due to size)

Supplementary Table 4. List of BRAF (fusion) gene and GFP-specific primers. Primer used for breakpoint PCR, HA-tag spanning PCR and for the gateway cloning

S1. Impact of BRAF (fusion) gene expression on phosphorylation of AKT. S2. BRAF (fusion) gene mRNA and protein expression levels. S3. Phosphoproteomics screen in HEK293 cells reveals that BRAF fusions and BRAFV600E activate similar signaling pathways. S4. BRAF (fusion) gene expression and MAPK pathway activation in HEK293 cells. S5. BRAF (fusion) protein localization in HEK293 cells. S6. Establishment of optimal duration of dox induction for BRAF (fusion) protein expression. S7. Validation of phospho-proteins and transcriptomic analysis of BRAF (fusion) gene expressing P18T CRC organoid lines. S8. Expression of most differentially expressed genes in DLG1-BRAF expressing P18T organoids and CRC patients. S9. BRAF (fusion) genes confer resistance to EGFR inhibition. S10. Impact of afatinib exposure on pAKT levels in BRAF (fusion) gene expressing CRC organoids. S11. Differential sensitivities of BRAF (fusion) genes to combinatorial targeting of EGFR and MEK.

Supplementary Materials and Methods