Targetable BRAF and RAF1 Alterations in Advanced Pediatric Cancers

Abstract

RAF family protein kinases signal through the MAPK pathway to orchestrate cellular proliferation, survival, and transformation. Identifying BRAF alterations in pediatric cancers is critically important as therapeutic agents targeting BRAF or MEK may be incorporated into the clinical management of these patients. In this study, we performed comprehensive genomic profiling on 3,633 pediatric cancer samples and identified a cohort of 221 (6.1%) cases with known or novel alterations in BRAF or RAF1 detected in extracranial solid tumors, brain tumors, or hematological malignancies. Eighty percent (176/221) of these tumors had a known-activating short variant (98, 55.7%), fusion (72, 40.9%), or insertion/deletion (6, 3.4%). Among BRAF altered cancers, the most common tumor types were brain tumors (74.4%), solid tumors (10.8%), hematological malignancies (9.1%), sarcomas (3.4%), and extracranial embryonal tumors (2.3%). RAF1 fusions containing intact RAF1 kinase domain (encoded by exons 10-17) were identified in seven tumors, including two novel fusions TMF1-RAF1 and SOX6-RAF1. Additionally, we highlight a subset of patients with brain tumor with positive clinical response to BRAF inhibitors, demonstrating the rationale for incorporating precision medicine into pediatric oncology. IMPLICATIONS FOR PRACTICE: Precision medicine has not yet gained a strong foothold in pediatric cancers. This study describes the landscape of BRAF and RAF1 genomic alterations across a diverse spectrum of pediatric cancers, primarily brain tumors, but also encompassing melanoma, sarcoma, several types of hematologic malignancy, and others. Given the availability of multiple U.S. Food and Drug Administration-approved BRAF inhibitors, identification of these alterations may assist with treatment decision making, as described here in three cases of pediatric cancer.

Keywords: Biomarkers; Brain neoplasms; Leukemia; Pediatrics; Precision medicine; Proteins B-raf; Proto-oncogene; Tumor.

Figure 1

Landscape of known‐activating BRAF alterations. (A): Schematic diagram of domains and alterations of BRAF. (B): Schematic of known‐activating BRAF fusions, including those identified in this study (STARD3NL‐BRAF and KHDRBS2‐BRAF). Exon numbers at the fusion boundary are depicted below each fusion diagram.Abbreviation: CR, conserved region.

Figure 2

Genomic landscape of hematological malignancies and extracranial solid tumors with a known‐activating BRAF alteration. Specimens are arranged from young to old (left to right) within each cancer type.Abbreviations: AML, acute myeloid leukemia; MPNST, malignant peripheral nerve sheath tumor; MSI, microsatellite instability; MSS, microsatellite stable; mut/Mb, mutations per megabase; NOS, not otherwise specified; TMB, tumor mutational burden.

Figure 3

Genomic landscape of primary brain tumors bearing a known‐activating BRAF short variant or indel. Specimens are arranged from young to old (left to right) within each cancer type. Blue star indicates the genomic profile associated with Index Case 1.Abbreviations: G, grade; GBM, glioblastoma; HGG, high grade glioma; HGGNT, high grade glioneuronal tumor; LGG, low‐grade glioma; LGGNT, low grade glioneuronal tumor; MSI, microsatellite instability; MSS, microsatellite stable; mut/Mb, mutations per megabase; NOS, not otherwise specified; PA, pilocytic astrocytoma; PXA, pleomorphic xanthoastrocytoma; TMB, tumor mutational burden; WHO, World Health Organization.

Figure 4

Genomic landscape of primary brain tumors bearing a known‐activating BRAF fusion. Specimens are arranged from young to old (left to right) within each cancer type.Abbreviations: CNS‐PNET, central nervous system–primitive neuroectodermal tumor; DA, diffuse astrocytoma; DIGG, desmoplastic infantile ganglioglioma; DOLT, disseminated oligodendroglial‐like leptomeningeal tumor; G, grade; HGG, high grade glioma; LGG, low‐grade glioma; LGGNT, low grade glioneuronal tumor; MSI, microsatellite instability; MSS, microsatellite stable; mut/Mb, mutations per megabase; NOS, not otherwise specified; PA, pilocytic astrocytoma; PXA, pleomorphic xanthoastrocytoma; TMB, tumor mutational burden; WHO, World Health Organization.

Figure 5

Landscape of BRAF nonfusion rearrangements. (A): Description of BRAF rearrangements in pediatric malignancy. (B): Schematic representing loss of BRAF exons 1–7. (C): Genomic landscape of pediatric cancers bearing a BRAF nonfusion rearrangement.Abbreviations: G, grade; LGG, low‐grade glioma; MSI, microsatellite instability; MSS, microsatellite stable; mut/Mb, mutations per megabase; NOS, not otherwise specified; PA, pilocytic astrocytoma; TMB, tumor mutational burden.

Figure 6

Landscape of RAF fusions. (A): Hematoxylin and eosin staining and corresponding schematics representing recurrent and novel RAF1 kinase fusions identified in pediatric cancer. Exon numbers at the fusion boundary are depicted below each fusion diagram. (B): Genomic landscape of pediatric cancers bearing a known‐activating RAF1 fusion. Specimens are arranged from young to old (left to right) within each cancer type.Abbreviations: MSI, microsatellite instability; MSS, microsatellite stable; mut/Mb, mutation; mutations per megabase; NOS, not otherwise specified; TMB, tumor mutational burden.

Figure 7

Postcontrast magnetic resonance imaging images showing decrease in tumor size in three separate BRAF V600E–positive pediatric patients after treatment with vemurafenib.Abbreviations: BID, bis in die (twice daily); GBM, glioblastoma; MRI, magnetic resonance imaging; PO, per os (by mouth); WHO, World Health Organization.