Abstract 1248: DNA methylation biomarkers for MPNST detection in patients with neurofibromatosis type 1

Malignant peripheral nerve sheath tumors (MPNSTs) are a highly aggressive soft tissue sarcoma affecting approximately 10-15% of individuals with neurofibromatosis type 1 (NF1). MPNST development is characterized by an altered DNA methylation landscape and presents a promising area for developing MPNST-specific biomarkers for screening NF1 patients in the clinic. Here, using genome-wide DNA methylation profiling of a cohort of 13 matched pairs of MPNSTs and adjacent neurofibroma tissues, along with MPNST cell lines and control samples, we conducted intensive DNA methylation analysis towards identification and validation of candidate MPNST specific CpG sites. We utilized a logistic regression model with LASSO regularization to identify the best candidate biomarkers for MPNST detection in patient tissue and/or blood samples. For model fitting, we used TCGA data along with an independent, publicly available dataset. The selected candidate biomarkers were validated on an independent cohort of 22 tissue samples using bisulfite sequencing as well as optimized droplet digital PCR (ddPCR). Our comprehensive analysis revealed the presence of a unique hypermethylation pattern during MPNST development that is also recapitulated within the in vitro MPNST model. Further, based on application of stringent feature selection criteria among an MPNST and NF comparison, together with building a prediction model, we provide a list of candidate MPNST-specific CpGs. Moreover, we successfully applied a ddPCR method to measure the DNA level of five selected candidate biomarkers, all of which showed high performance for MPNST detection (sensitivity: >88%, specificity: >91%) in tissue samples. Overall, our findings confirmed the appearance of a unique hypermethylation pattern during malignant transformation that is also maintained across an in vitro MPNST model. Importantly, we provide a panel of candidate CpGs that have great potential to be further applied as biomarkers in clinical settings for MPNST detection in NF1 patients' tissue and/or liquid biopsy samples. Citation Format: Katarzyna J. Tomczak, Christine B. Peterson, S Carson Callahan, Sharon M. Landers, Christopher J. Terranova, Gabryella S. Serrao, Angela D. Bhalla, Jace P. Landry, Zachary A. Mulder, Michelle G. Yeagley, Ayush T. Raman, Erica L. Gardenhire, Davis R. Ingram, Alexander Lazar, Wei-Lien Wang, Ian E. McCutcheon, John M. Slopis, Kunal Rai, Keila E. Torres. DNA methylation biomarkers for MPNST detection in patients with neurofibromatosis type 1 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1248.