Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development

Abstract

Renal angiomyolipoma is a kidney tumor in the perivascular epithelioid (PEComa) family that is common in patients with Tuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) but occurs rarely sporadically. Though histologically benign, renal angiomyolipoma can cause life-threatening hemorrhage and kidney failure. Both angiomyolipoma and LAM have mutations in TSC2 or TSC1. However, the frequency and contribution of other somatic events in tumor development is unknown. We performed whole exome sequencing in 32 resected tumor samples (n = 30 angiomyolipoma, n = 2 LAM) from 15 subjects, including three with TSC. Two germline and 22 somatic inactivating mutations in TSC2 were identified, and one germline TSC1 mutation. Twenty of 32 (62%) samples showed copy neutral LOH (CN-LOH) in TSC2 or TSC1 with at least 8 different LOH regions, and 30 of 32 (94%) had biallelic loss of either TSC2 or TSC1. Whole exome sequencing identified a median of 4 somatic non-synonymous coding region mutations (other than in TSC2/TSC1), a mutation rate lower than nearly all other cancer types. Three genes with mutations were known cancer associated genes (BAP1, ARHGAP35 and SPEN), but they were mutated in a single sample each, and were missense variants with uncertain functional effects. Analysis of sixteen angiomyolipomas from a TSC subject showed both second hit point mutations and CN-LOH in TSC2, many of which were distinct, indicating that they were of independent clonal origin. However, three tumors had two shared mutations in addition to private somatic mutations, suggesting a branching evolutionary pattern of tumor development following initiating loss of TSC2. Our results indicate that TSC2 and less commonly TSC1 alterations are the primary essential driver event in angiomyolipoma/LAM, whereas other somatic mutations are rare and likely do not contribute to tumor development.

Hepatic angiomyolipoma: mutation analysis and immunohistochemical pitfalls in diagnosis

“…All five tested cases of hepatic AML in our series showed TSC2 gene mutations, with bi‐allelic mutations in four cases. Based on our series, as well as reported results in the literature, the TSC2 mutation is perhaps a universal finding in sporadic AMLs and is probably sufficient for tumorigenesis, as other genetic events are rare. TSC2 mutations are scattered throughout the gene and mutations in 40 of 41 exons have been reported .…”

“…TSC1/TSC2 ‐encoded proteins (hamartin and tuberin) modulate cell functions through the mTOR signalling, and also regulate cell growth and proliferation. Germline mutations in TSC1 or TSC2 are observed in AMLs occurring in tuberous sclerosis, while TSC2 mutations have been described in sporadic renal AMLs . Mutational analysis by sequencing has not been reported in sporadic hepatic AMLs, but loss of heterozygosity (LOH) at the TSC2 site has been described .…”

The concept of type 2 segmental mosaicism, expanding from dermatology to general medicine

“…In most cases, however, the involvement of lungs is diffuse and bilateral, which should be taken as an argument against T2SM. The same is true for the TSC‐associated angiomyolipomas of kidneys . The involvement is likewise bilateral in most cases.…”

Familial pneumothorax: towards precision medicine

“…These encode tumour suppressors, and so loss of heterozygosity or inactivation of the wild-type allele, which almost always occurs via somatic mutational events, can lead to hamartoma development in a variety of organs, typically the brain, kidney, skin, retina and lung 40. The relevance of tuberous sclerosis to pneumothorax stems from its strong association with lymphangioleiomyomatosis (LAM).…”