Somatic activating BRAF variants cause isolated lymphatic malformations

Abstract

Somatic activating variants in PIK3CA, the gene that encodes the p110α catalytic subunit of phosphatidylinositol 3-kinase (PI3K), have been previously detected in ∼80% of lymphatic malformations (LMs).^{1 , 2} We report the presence of somatic activating variants in BRAF in individuals with LMs that do not possess pathogenic PIK3CA variants. The BRAF substitution p.Val600Glu (c.1799T>A), one of the most common driver mutations in cancer, was detected in multiple individuals with LMs. Histology revealed abnormal lymphatic channels with immunopositivity for BRAF^V600E in endothelial cells that was otherwise indistinguishable from PIK3CA-positive LM. The finding that BRAF variants contribute to low-flow LMs increases the complexity of prior models associating low-flow vascular malformations (LM and venous malformations) with mutations in the PI3K-AKT-MTOR and high-flow vascular malformations (arteriovenous malformations) with mutations in the RAS-mitogen-activated protein kinase (MAPK) pathway.³ In addition, this work highlights the importance of genetic diagnosis prior to initiating medical therapy as more studies examine therapeutics for individuals with vascular malformations.

Keywords: BRAF; PIK3CA; VANSeq; clinical diagnostics; ddPCR; endothelium; lymphatic malformation; mosaicism; post-zygotic; vascular.

Figure 1

Clinical features of BRAF-mutated LM and confirmation of genetic diagnosis (A–G) Clinical photos of LR17-322 (A) and LR19-346 (C), showing posterior neck LMs. Corresponding computed tomography (CT) (LR17–322; B) and MRI (LR19-346, D; LR19-443, E) images demonstrate macrocystic lesions with minimal septations of the posterior lateral neck and axilla. Integrated Genomics Viewer image for LR19-346 demonstrates somatic BRAF p.Val600Glu variant (F), confirmed on droplet digital PCR (G). (H) Variant concentration image from Quantasoft shows variability in mutation prevalence between samples (H). Note: (A) and (B) were previously published prior to identification of this individual’s genetic variant.

Figure 2

Histology and immunohistochemistry of PIK3CA and BRAF mutated LMs LM tissue from two individuals with BRAF p.Val600Glu substitutions (A–F) and one individual with PIK3CA p.His1047Arg substitution. (G–I). H&E stains (A), (D), and (G) show dilated cystic channels with bland, flattened epithelium. (B), (E), and (H) show presence of podoplanin (a.k.a. D2-40) immunoreactivity in endothelial cells. Panels on the right show BRAF p.Val600Glu immunoreactivity (VE1 staining) in endothelial cells in BRAF mutant LM (C and F), but not in PIK3CA mutant LM (I).