Ultrasensitive profiling of UV-induced mutations identifies thousands of subclinical facial tumors in tuberous sclerosis complex

• Published in: The Journal of clinical investigation Vol. 132; no. 10; pp. 1 - 16
• Main Authors: Klonowska, Katarzyna, Grevelink, Joannes M., Giannikou, Krinio, Ogorek, Barbara A., Herbert, Zachary T., Thorner, Aaron R., Darling, Thomas N., Moss, Joel, Kwiatkowski, David J.
• Format: Journal Article
• Language: English
• Published: United States American Society for Clinical Investigation 15.05.2022
• Subjects: Biomedical research; Biopsy; Capillary electrophoresis; Cell culture; Clinical Medicine; Complications and side effects; Connective tissue tumors; Dermatology; Development and progression; Face; Facial Neoplasms - genetics; Fibroblasts; Gene deletion; Gene frequency; Gene mutations; Genetic aspects; Genetics; Head & neck cancer; Head and neck tumors; Health aspects; Humans; Medical research; Medicine, Experimental; Mutation; Nucleotides; p53 Protein; Risk factors; Skin; Tuberous sclerosis; Tuberous Sclerosis - diagnosis; Tuberous Sclerosis - genetics; Tuberous Sclerosis - pathology; Tuberous Sclerosis Complex 1; Tuberous Sclerosis Complex 1 Protein - genetics; Tuberous Sclerosis Complex 2; Tuberous Sclerosis Complex 2 Protein - genetics; Tumor Suppressor Proteins - genetics; Tumors; Ultraviolet radiation; United States; Genetics; Molecular genetics; Dermatology; Tumor suppressors; Skin cancer
• ISSN: 1558-8238; 0021-9738; 1558-8238
• DOI: 10.1172/JCI155858

BackgroundTuberous sclerosis complex (TSC) is a neurogenetic syndrome due to loss-of-function mutations in TSC2 or TSC1, characterized by tumors at multiple body sites, including facial angiofibroma (FAF). Here, an ultrasensitive assessment of the extent and range of UV-induced mutations in TSC facial skin was performed.MethodsA multiplex high-sensitivity PCR assay (MHPA) was developed, enabling mutation detection at extremely low (<0.1%) variant allele frequencies (VAFs).ResultsMHPA assays were developed for both TSC2 and TP53, and applied to 81 samples, including 66 skin biopsies. UV-induced second-hit mutation causing inactivation of TSC2 was pervasive in TSC facial skin with an average of 4.8 mutations per 2-mm biopsy at median VAF 0.08%, generating more than 150,000 incipient facial tumors (subclinical "micro-FAFs") in the average TSC subject. The MHPA analysis also led to the identification of a refined UV-related indel signature and a recurrent complex mutation pattern, consisting of both a single-nucleotide or dinucleotide variant and a 1- to 9-nucleotide deletion, in cis.ConclusionTSC facial skin can be viewed as harboring a patchwork of clonal fibroblast proliferations (micro-FAFs) with indolent growth, a small proportion of which develop into clinically observable FAF. Our observations also expand the spectrum of UV-related mutation signatures.FundingThis work was supported by the TSC Alliance; the Engles Family Fund for Research in TSC and LAM; and the NIH, National Heart, Lung, and Blood Institute (U01HL131022-04 and Intramural Research Program).