Abstract 979: Cell-free DNA fragmentomics and second malignant neoplasm risk in patients with PTEN hamartoma tumor syndrome

Abstract

Abstract Individuals with PTEN hamartoma tumor syndrome (PHTS) harbor germline PTEN variants that confer a significantly increased lifetime risk of various organ-specific cancers, and a 7-fold increased risk of second primary malignant neoplasms (SMNs). Currently, there is no reliable biomarker that can accurately predict which individuals with PHTS will develop malignancies, let alone SMN. Currently, there is no reliable biomarker that can accurately predict which individuals with PHTS will develop malignancies, let alone SMN. Despite the highly promising value of cell-free DNA (cfDNA) as a biomarker for underlying sporadic cancers, the utility of cfDNA in individuals with hereditary forms of cancer remains poorly understood. Thus, we performed a retrospective study in prospectively accrued patients with PHTS investigating whether plasma cfDNA profiles can be leveraged as a predictive marker of cancer risk. We performed ultra-low pass whole genome sequencing of cfDNA of archived plasma samples from patients with PHTS without cancer (N = 50), and those with cancer (N = 49). Those with cancer included patients with only a single primary malignant neoplasm (PMN, N = 23) and patients with second malignant neoplasms (SMN, N = 26). To investigate cfDNA profiles in patients with PHTS and subclinical cancer, we included nine patients with plasma archived before their cancer diagnosis. We observed that patients with PHTS and SMNs have significantly decreased proportion of di- and tri-nucleosome-associated cfDNA fragments compared to patients with PMNs and those without cancer. Furthermore, SMN status was associated with increased genome-wide fragmentation (ratio of short to long fragments) of mono- (OR 2.37, 95% CI [1.09, 7.27]; P = 0.025) and di-nucleosome-associated (OR 3.03, 95% CI [1.07, 15.7]; P = 0.029) cfDNA fragments, even after controlling for age at plasma draw and phenotypic burden. Fragment end profiling was performed by calculating the frequencies of the first 4-nucleotide sequence (4-mer end motif) at each 5’ end of cfDNA fragments. We identified 35 differentially abundant 4-mer end motifs when comparing patients with SMN to those without cancer. Patients with PHTS and SMNs were characterized by a decrease in A-end motifs with concurrent increases in G- and T-end motifs. Increased frequency of C-motifs—namely CC- and CA-end motifs—appeared to be unique to patients who had plasma drawn before their SMN diagnosis, a potential marker for active cancer. Our findings provide evidence that cfDNA fragmentomic features can be leveraged as a potential marker of individual SMN risk in PHTS. These results may facilitate earlier cancer detection and intervention as well as prevent unnecessary high-risk cancer surveillance and prophylactic surgeries in this vulnerable population. Citation Format: Darren Liu, Lamis Yehia, Andrew Dhawan, Ying Ni, Charis Eng. Cell-free DNA fragmentomics and second malignant neoplasm risk in patients with PTEN hamartoma tumor syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 979.