Abstract P5-05-03: Characterization of the genomic landscape of breast carcinoma patients with NF1 alterations using comprehensive cell-free tumor DNA next-generation sequencing
Authors: Chang Eric , Tsai Jill , Lim Bora 
Published: March 2023

Background: NF1 (neurofibromin type 1) encodes neurofibromin, and is commonly altered in many cancers, including breast cancer. NF1 suppresses breast cancer by not only negatively regulating RAS signaling but also by independently acting as a transcriptional co-repressor of the estrogen receptor (ER). In this study, we analyzed the genomic landscape of patients with NF1 alterations from a large genomic database to define what unique patient characteristics were associated with NF1 alterations. Methods: Retrospective analysis of the Guardant Health database based on samples from the commercially available Guardant360® plasma-based circulating tumor DNA (ctDNA) assay. Samples were queried between June 2020-June 2022 for patients with any detected NF1 alteration and breast cancer diagnosis. NF1 synonymous alterations were excluded from this study. Statistics were conducted using a two-sided Fisher’s exact test. Results: NF1 alterations were found in 895 patients with breast cancer over 1156 samples, typically in female patients (98.2%) diagnosed with breast carcinoma (99.4%). The average age of patients was 66 years old (23-93), with a median of 1.4 serial tests (1-19). The common nonsynonymous NF1 alterations are missense mutations (56.5%), nonsense mutations (23.5%), indels (22.3%), and aberrant splicing mutations (8.2%). There were significant differences in NF1 alteration frequency between younger (&lt; 55 y/o) vs. older (≤55 y/o) patients, with older patients demonstrating an increase in NF1 alterations (p&lt; 0.0001) across all mutation types except for splice mutations. There was also a significant difference in NF1 alterations between female vs. male patients, with male patients trending toward a higher frequency in NF1 missense alterations. Mutations affecting genes encoding the receptor tyrosine kinase (e.g., HER2) and the Ras-MAP kinase pathways (e.g., several RAS and RAF genes) co-occur with NF1 mutations. In contrast, there is no evidence of co-occurrence with mutations in the ESR1 gene, which encodes ER. The blood tumor mutational burden (bTMB) score was evaluable in 848 patients with an average score of 26.1 mut/Mb (range 1.16-447.7). In addition, mutations affecting genes controlling the cell cycle were also found to co-occur with NF1 mutations. Conclusions: Plasma-based liquid biopsy via G360 can efficiently identify NF1 alterations illustrating that such genetic alterations are common in this metastatic breast cancer cohort. Analysis of co-occurrent mutations supports our model that a key role of NF1 is to act as an ER transcriptional co-repressor, such that its loss is functionally redundant with acquiring ESR1 mutations. Oncogenic activation of the RTK-Ras pathways is needed for efficient progression to metastasis by additional mutations in this pathway. Mutational co-occurrence may also identify collaborating molecular events that collaborate with NF1 loss to promote treatment relapse and metastasis.

Citation Format: Eric Chang, Jill Tsai, Bora Lim. Characterization of the genomic landscape of breast carcinoma patients with NF1 alterations using comprehensive cell-free tumor DNA next-generation sequencing [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-05-03.