Abstract 3678: Liquid biopsy fragmentomics approach for the diagnosis of uterine tumors
Authors: Meagan S. Cobb, Philippe Jolivet, Kristen N. Ganjoo, Deirdre A. Lum, Matt van de Rijn, Joanna Przybyl
Journal: Cancer Research (2025)

Abstract Background: Leiomyomas (LM), also known as fibroids, are common benign tumors of the smooth muscle of the uterus that can cause pain, infertility, and abnormal menstrual bleeding. Diagnosing LM is challenging using clinical indications alone, as they share symptoms with leiomyosarcoma (LMS), a rare, aggressive uterine malignancy with a ∼50% disease-specific survival. Pre-operative distinction between LM and LMS is difficult because these tumors are rarely biopsied before surgery. We hypothesize that a non-invasive circulating tumor DNA (ctDNA) test based on LMS- and LM-specific molecular markers will provide accurate pre-operative diagnosis and guide appropriate surgical treatment. Methods: We previously analyzed point mutations and copy number alterations (CNAs) in ctDNA using deep targeted sequencing and shallow whole-genome sequencing (WGS) from plasma specimens of 7 LMS and 12 LM patients (PMIDs: 29463554, 32232185). To build on this, we performed a new analysis of the first 4 nucleotide sequences (4-mer motifs) on the 5’ end of the cell-free DNA fragments using shallow WGS data. The frequency of 256 possible 4-mer motifs was calculated using R programming and normalized to total reads in each specimen. Two-class differential analysis identified motifs enriched in LM and LMS (false discovery rate &amp;lt; 0.05). Results: Our previous studies demonstrated the feasibility of ctDNA detection in LMS and LM patients. In LMS patients, ctDNA was detected in 6 of 7, with &amp;gt;98% specificity; in LM patients, ctDNA was detected in 6 of 12, with 76% specificity. To increase ctDNA detection sensitivity, we incorporated fragmentomics as a new ctDNA marker. Our new analysis identified 66 significantly enriched and 21 significantly decreased motifs in cell-free DNA from LMS patients compared to LM patients. Motifs associated with DNASE1L3 nuclease activity (e.g., CCCA) were significantly decreased in LM compared to LMS patients. Conclusion: We identified new tumor-specific fragmentomic markers in cell-free DNA from LMS and LM patients. Combining detection of point mutations, CNAs, and fragmentomic patterns could enable a highly sensitive ctDNA assay for accurate pre-operative distinction between LM and LMS. Next, we will validate DNASE1L3 and other nucleases in tissue microarrays of 100+ LM and 200+ LMS specimens by immunohistochemistry, and validate distinct fragmentomic patterns using expanded plasma collections. This research addresses an unmet clinical need for accurate pre-operative diagnosis of uterine tumors. Citation Format: Meagan S. Cobb, Philippe Jolivet, Kristen N. Ganjoo, Deirdre A. Lum, Matt van de Rijn, Joanna Przybyl. Liquid biopsy fragmentomics approach for the diagnosis of uterine tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3678.