Targeted Next Generation Sequencing Expands Genotype in Patients with PIK3CA-Related Overgrowth Spectrum (PROS)

Background: Disorders of somatic mosaicism (DoSM) are caused by mutations that arise post-zygotically and are present in only a specific part of the body. These mutations alter the function and regulation of key genes in cell proliferation pathways, including the PI3K/AKT/mTOR pathway, and show significant overlap with mutations identified in cancer(McNulty et al. Am J Hum Genet, 2019). PIK3CA-Related Overgrowth Spectrum (PROS) is an umbrella term that encompasses a variety of overgrowth syndromes caused by post-zygotic, somatic gain-of-function PIK3CA mutations with low-level mosaicism (Luks et al. J Pediatr, 2015). The clinical phenotype of PROS is heterogeneous and many tissue types can be affected. This often makes clinical diagnosis challenging. The use of cancer genomics in patients with vascular anomalies may aid in establishing a genetic diagnosis and expand use of targeted medical therapies.

Methods: Three patients who presented with clinical symptoms of PROS underwent targeted next generation sequencing of affected tissue using OncoPanel. Oncopanel is a genomic assay that detects somatic mutations, copy number variations and structural variants in 447 genes implicated in cancer.

Results: Three patients with a PROS phenotype demonstrated somatic mutations in genes distinct from PIK3CA.

Case 1: A 15-year-old female presented with a painful right leg mass, calf atrophy, contracture of the knee, leg-length discrepancy, and severe limp. Histology was consistent with fibroadipose vascular anomaly (FAVA) versus kaposiform hemangioendothelioma (KHE). Given her significant functional impairment, treatment with Sirolimus was initiated with significant improvement in appearance and functionality. OncoPanel testing revealed a PIK3C2B c.2881G>A (p.G961S) mutation.

Case 2: A 12-month-old male was noted at birth to have a diffuse capillary malformation, multiple lymphatic malformations, macrodactyly of his bilateral hands and leg length-discrepancy, consistent with Congenital Lipomatous Overgrowth, Vascular Malformations, Epidermal Nevi, Spinal/Skeletal Anomalies/Scoliosis (CLOVES) syndrome. He underwent numerous surgical de-bulking procedures, epiphysiodesis, sclerotherapy, and laser therapy with continued disease progression. OncoPanel revealed a PIK3R1c.1731_1738delAGACCAATinsATGTAAGAAAG (p.D578_Y580delinsCKKD) mutation.

Case 3: A 10-month-old female presented with a diffuse capillary malformation and leg-length discrepancy. She subsequently developed multiple painful and progressive lymphatic lesions over her left arm and chest which did not respond to sclerotherapy. Due to high clinical suspicion for PROS, she underwent targeted genetic testing via droplet digital PCR (ddPCR) to detect the five most common variants (C420R, E542K, E545K, H1047L, H1047R) in PIK3CA, but no hotspot mutations were identified. Over the next year and a half, the patient had two biopsies performed, PIK3CA ddPCR testing performed twice, and OncoPanel testing performed twice. OncoPanel testing of the second tissue biopsy ultimately resulted in the identification of a PIK3R1 c.1723-1731del p.K575_R577del mutation.

Conclusion: The clinical diagnosis of DoSM is often challenging. While the use of cancer genomics for diagnostic purposes in vascular anomalies is uncommon, its use continues to broaden our understanding of syndromes related to alterations in the PI3K/AKT/mTOR pathway. PIK3CB encodes a catalytic subunit of PI3K, p110β, and is dysregulated in certain types of cancer. PIK3R1 encodes multiple regulatory subunits of PI3K and acts as a negative regulator of PIK3CA function. Both gain-of-function of PIK3CB or loss-of-function of PIK3R1 lead to inappropriate activation of PIK3CA, and our cases highlight that mutations in other genes can lead to the clinical phenotype of PROS. It is reasonable to expect that patients with alterations in genes that activate PIK3CA may benefit from medical treatment with direct PIK3CA inhibitors. Limiting diagnostic testing to evaluation of the PIK3CA gene alone may yield negative results and preclude patient eligibility for treatment with novel therapies. The use of next-generation sequencing (NGS) designed to detect somatic variations in cancer will likely play a pivotal role in detecting variants in vascular anomalies in the future and in expanding our understanding of genetic alterations involved in PROS.