Unveiling a BRAF Signature Proficient in Accurately Capturing Oncogenic Activity and Guiding Prognostic Prediction Across Multiple Cancers

Abstract

Although BRAF is frequently mutated across multiple cancer types, its clinical utility as a prognostic biomarker has remained inconsistent in clinical practice, likely due to additional events modulating BRAF signaling pathways. This inconsistency has driven our investigation into the broader landscape of BRAF signaling and the development of a robust molecular signature to assess BRAF-driven oncogenic activity. To achieve this, we introduced BRAF25, a transcriptional signature designed to effectively capture BRAF oncogenic activity. Our findings reveal that 25.6% of TCGA colorectal cancer (CRC) tumors exhibit BRAF pathway activation, even in 19.4% of BRAF wild-type (WT) cases, suggesting alternative mechanisms driving pathway activation. The BRAF-active subtype, termed BAG-3 (BRAF Activity Group-3), demonstrated reduced responsiveness to chemotherapy and anti-BRAF therapy. Notably, BRAF25 subtyping addresses the limitations of using BRAF mutation alone to predict patient survival. We experimentally screened and validated DUSP6 as a sensitizing target for anti-BRAF therapy, enhancing BRAF inhibitor efficacy in CRC. Furthermore, pan-cancer analyses implicate the BRAF25 signature in poor prognosis across diverse BRAF-driven malignancies. In conclusion, stratifying patients by transcriptional BRAF oncogenic activity, instead of relying solely on BRAF mutation status, provides a more precise approach to guide clinical decision-making and improve therapeutic outcomes.

Keywords

BRAF mutation / BRAF oncogenic activity / DUSP6 / gene signature / prognostic prediction

References

[1] R. Ullah, Q. Yin, A. H. Snell, and L. Wan, “RAF-MEK-ERK Pathway in Cancer Evolution and Treatment,” Seminars in Cancer Biology 85 (2022): 123–154.

[2] P. J. Roberts and C. J. Der, “Targeting the Raf-MEK-ERK Mitogen-Activated Protein Kinase Cascade for the Treatment of Cancer,” Oncogene 26, no. 22 (2007): 3291–3310.

[3] H. Davies, G. R. Bignell, C. Cox, et al., “Mutations of the BRAF Gene in Human Cancer,” Nature 417, no. 6892 (2002): 949–954.

[4] P. Bhatia, P. Friedlander, E. A. Zakaria, and E. Kandil, “Impact of BRAF Mutation Status in the Prognosis of Cutaneous Melanoma: An Area of Ongoing Research,” Annals of Translational Medicine 3, no. 2 (2015): 24.

[5] I. J. Fernandez, O. Piccin, S. Sciascia, et al., “Clinical Significance of BRAF Mutation in Thyroid Papillary Cancer,” Otolaryngology – Head and Neck Surgery 148, no. 6 (2013): 919–925.

[6] K. P. Hoeflich, D. C. Gray, M. T. Eby, et al., “Oncogenic BRAF Is Required for Tumor Growth and Maintenance in Melanoma Models,” Cancer Research 66, no. 2 (2006): 999–1006.

[7] D. Dankort, D. P. Curley, R. A. Cartlidge, et al., “Braf(V600E) Cooperates With Pten Loss to Induce Metastatic Melanoma,” Nature Genetics 41, no. 5 (2009): 544–552.

[8] A. M. Menzies and G. V. Long, “Dabrafenib and Trametinib, Alone and in Combination for BRAF-Mutant Metastatic Melanoma,” Clinical Cancer Research 20, no. 8 (2014): 2035–2043.

[9] R. Roskoski, “Targeting Oncogenic Raf Protein-Serine/Threonine Kinases in human Cancers,” Pharmacological Research 135 (2018): 239–258.

[10] A. Grothey, M. Fakih, and J. Tabernero, “Management of BRAF-Mutant Metastatic Colorectal Cancer: A Review of Treatment Options and Evidence-Based Guidelines,” Annals of Oncology 32, no. 8 (2021): 959–967.

[11] R. B. Corcoran, H. Ebi, A. B. Turke, et al., “EGFR-Mediated Re-Activation of MAPK Signaling Contributes to Insensitivity of BRAF Mutant Colorectal Cancers to RAF Inhibition With Vemurafenib,” Cancer Discovery 2, no. 3 (2012): 227–235.

[12] A. Prahallad, C. Sun, S. Huang, et al., “Unresponsiveness of Colon Cancer to BRAF(V600E) Inhibition Through Feedback Activation of EGFR,” Nature 483, no. 7387 (2012): 100–103.

[13] H. Shi, W. Hugo, X. Kong, et al., “Acquired Resistance and Clonal Evolution in Melanoma During BRAF Inhibitor Therapy,” Cancer Discovery 4, no. 1 (2014): 80–93.

[14] J. E. Faris and D. P. Ryan, “Trees, Forests, and Other Implications of a BRAF Mutant Gene Signature in Patients With BRAF Wild-Type Disease,” Journal of Clinical Oncology 30, no. 12 (2012): 1255–1257.

[15] S. In 't Veld, K. N. Duong, M. Snel, et al., “A Computational Workflow Translates a 58-Gene Signature to a Formalin-Fixed, Paraffin-Embedded Sample-Based Companion Diagnostic for Personalized Treatment of the BRAF-Mutation-Like Subtype of Colorectal Cancers,” High Throughput 6, no. 4 (2017): 16.

[16] J. M. Dolezal, A. Trzcinska, C. Y. Liao, et al., “Deep Learning Prediction of BRAF-RAS Gene Expression Signature Identifies Noninvasive Follicular Thyroid Neoplasms With Papillary-Like Nuclear Features,” Modern Pathology 34, no. 5 (2021): 862–874.

[17] K. Yao, E. Zhou, and C. Cheng, “A B-Raf V600E Gene Signature for Melanoma Predicts Prognosis and Reveals Sensitivity to Targeted Therapies,” Cancer Medicine 11, no. 4 (2022): 1232–1243.

[18] C. Kannengiesser, A. Spatz, S. Michiels, et al., “Gene Expression Signature Associated With BRAF Mutations in Human Primary Cutaneous Melanomas,” Molecular Oncology 1, no. 4 (2008): 425–430.

[19] J. Sasame, N. Ikegaya, M. Kawazu, et al., “HSP90 Inhibition Overcomes Resistance to Molecular Targeted Therapy in BRAFV600E-Mutant High-Grade Glioma,” Clinical Cancer Research 28, no. 11 (2022): 2425–2439.

[20] D. J. L. Coleman, P. Keane, R. Luque-Martin, et al., “Gene Regulatory Network Analysis Predicts Cooperating Transcription Factor Regulons Required for FLT3-ITD+ AML Growth,” Cell Reports 42, no. 12 (2023): 113568.

[21] A. F. Ward, B. S. Braun, and K. M. Shannon, “Targeting Oncogenic Ras Signaling in Hematologic Malignancies,” Blood 120, no. 17 (2012): 3397–3406.

[22] D. Schaufler, D. F. Ast, H. L. Tumbrink, et al., “Clonal Dynamics of BRAF-Driven Drug Resistance in EGFR-mutant Lung Cancer,” Nature Partner Journals: Precision Oncology 5, no. 1 (2021): 102.

[23] S. Li, Y. Song, C. Quach, et al., “Transcriptional Regulation of Autophagy-Lysosomal Function in BRAF-Driven Melanoma Progression and Chemoresistance,” Nature Communications 10, no. 1 (2019): 1693.

[24] R. Rad, J. Cadinanos, L. Rad, et al., “A Genetic Progression Model of Braf(V600E)-Induced Intestinal Tumorigenesis Reveals Targets for Therapeutic Intervention,” Cancer Cell 24, no. 1 (2013): 15–29.

[25] P. Nieto, C. Ambrogio, and L. Esteban-Burgos, “A Braf Kinase-Inactive Mutant Induces Lung Adenocarcinoma,” Nature 548, no. 7666 (2017): 239–243.

[26] L. Ny, M. Hernberg, M. Nyakas, et al., “BRAF Mutational Status as a Prognostic Marker for Survival in Malignant Melanoma: A Systematic Review and Meta-Analysis,” Acta Oncology 59, no. 7 (2020): 833–844.

[27] T. Kambara, L. A. Simms, V. L. Whitehall, et al., “BRAF Mutation Is Associated With DNA Methylation in Serrated Polyps and Cancers of the Colorectum,” Gut 53, no. 8 (2004): 1137–1144.

[28] S. Rizzolio, S. Corso, S. Giordano, and L. Tamagnone, “Autocrine Signaling of NRP1 Ligand Galectin-1 Elicits Resistance to BRAF-Targeted Therapy in Melanoma Cells,” Cancers 12, no. 8 (2020): 2218.

[29] M. A. Hernandez, B. Patel, F. Hey, S. Giblett, H. Davis, and C. Pritchard, “Regulation of BRAF Protein Stability by a Negative Feedback Loop Involving the MEK-ERK Pathway but Not the FBXW7 Tumour Suppressor,” Cell Signalling 28, no. 6 (2016): 561–571.

[30] K. McGrail, P. Granado-Martinez, R. Esteve-Puig, et al., “BRAF Activation by Metabolic Stress Promotes Glycolysis Sensitizing NRAS(Q61)-Mutated Melanomas to Targeted Therapy,” Nature Communications 13, no. 1 (2022): 7113.

[31] S. J. Welsh, H. Rizos, R. A. Scolyer, and G. V. Long, “Resistance to Combination BRAF and MEK Inhibition in Metastatic Melanoma: Where to Next?,” European Journal of Cancer 62 (2016): 76–85.

[32] R. Nazarian, H. Shi, Q. Wang, et al., “Melanomas Acquire Resistance to B-RAF(V600E) Inhibition by RTK or N-RAS Upregulation,” Nature 468, no. 7326 (2010): 973–977.

[33] T. R. Wilson, J. Fridlyand, Y. Yan, et al., “Widespread Potential for Growth-Factor-Driven Resistance to Anticancer Kinase Inhibitors,” Nature 487, no. 7408 (2012): 505–509.

[34] B. Miao, Z. Ji, L. Tan, et al., “EPHA2 is a Mediator of Vemurafenib Resistance and a Novel Therapeutic Target in Melanoma,” Cancer Discovery 5, no. 3 (2015): 274–287.

[35] J. N. Anastas, R. M. Kulikauskas, T. Tamir, et al., “WNT5A Enhances Resistance of Melanoma Cells to Targeted BRAF Inhibitors,” Journal of Clinical Investigation 124, no. 7 (2014): 2877–2890.

[36] S. Caporali, A. Amaro, L. Levati, et al., “miR-126-3p Down-regulation Contributes to Dabrafenib Acquired Resistance in Melanoma by Up-Regulating ADAM9 and VEGF-A,” Journal of Experimental & Clinical Cancer Research 38, no. 1 (2019): 272.

[37] B. Valcikova, N. Vadovicova, K. Smolkova, et al., “eIF4F Controls ERK MAPK Signaling in Melanomas With BRAF and NRAS Mutations,” PNAS 121, no. 44 (2024): e2321305121.

[38] C. J. Caunt and S. M. Keyse, “Dual-Specificity MAP Kinase Phosphatases (MKPs): Shaping the Outcome of MAP Kinase Signalling,” FEBS Journal 280, no. 2 (2013): 489–504.

[39] T. Ito, M. J. Young, R. Li, et al., “Paralog Knockout Profiling Identifies DUSP4 and DUSP6 as a Digenic Dependence in MAPK Pathway-Driven Cancers,” Nature Genetics 53, no. 12 (2021): 1664–1672.

[40] C. W. Png, M. Weerasooriya, H. Li, et al., “DUSP6 Regulates Notch1 Signalling in Colorectal Cancer,” Nature Communications 15, no. 1 (2024): 10087.

[41] P. Riemer, A. Sreekumar, S. Reinke, et al., “Transgenic Expression of Oncogenic BRAF Induces Loss of Stem Cells in the Mouse Intestine, Which Is Antagonized by Beta-Catenin Activity,” Oncogene 34, no. 24 (2015): 3164–3175.

[42] K. P. Hoeflich, S. Herter, J. Tien, et al., “Antitumor Efficacy of the Novel RAF Inhibitor GDC-0879 Is Predicted by BRAFV600E Mutational Status and Sustained Extracellular Signal-Regulated Kinase/Mitogen-activated Protein Kinase Pathway Suppression,” Cancer Research 69, no. 7 (2009): 3042–3051.

[43] D. Rusinek, M. Swierniak, E. Chmielik, et al., “BRAFV600E-Associated Gene Expression Profile: Early Changes in the Transcriptome, Based on a Transgenic Mouse Model of Papillary Thyroid Carcinoma,” PLoS ONE 10, no. 12 (2015): e0143688.

[44] H. Lu, S. Liu, G. Zhang, et al., “Oncogenic BRAF-Mediated Melanoma Cell Invasion,” Cell Reports 15, no. 9 (2016): 2012–2024.

[45] J. D. G. Leach, N. Vlahov, P. Tsantoulis, et al., “Oncogenic BRAF, Unrestrained by TGFbeta-Receptor Signalling, Drives Right-sided Colonic Tumorigenesis,” Nature Communications 12, no. 1 (2021): 3464.

[46] T. J. Parmenter, M. Kleinschmidt, K. M. Kinross, et al., “Response of BRAF-Mutant Melanoma to BRAF Inhibition Is Mediated by a Network of Transcriptional Regulators of Glycolysis,” Cancer Discovery 4, no. 4 (2014): 423–433.

[47] M. Salvadores, F. Fuster-Tormo, and F. Supek, “Matching Cell Lines With Cancer Type and Subtype of Origin via Mutational, Epigenomic, and Transcriptomic Patterns,” Science Advances 6, no. 27 (2020): eaba1862.

[48] R. Kolde, S. Laur, P. Adler, and J. Vilo, “Robust Rank Aggregation for Gene List Integration and Meta-Analysis,” Bioinformatics 28, no. 4 (2012): 573–580.

[49] A. Bagaev, N. Kotlov, K. Nomie, et al., “Conserved Pan-Cancer Microenvironment Subtypes Predict Response to Immunotherapy,” Cancer Cell 39, no. 6 (2021): 845–865. e847.

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