Abstract 2294: Monitoring glioma treatment response through longitudinal analysis of cell-free DNA in cerebrospinal fluid: Insights from a comprehensive study using next-generation sequencing
Authors: Riviere-Cazaux Cecile, Xiaoxi Dong, Chao Dai, Wei Mo, Pan Du, Shidong Jia, Terence Burns
Journal: Cancer Research (2024)

Abstract Background: Assessing treatment response in gliomas with high fidelity remains challenging. Cell-free DNA (cfDNA) is increasingly recognized as a liquid biomarker in plasma and cerebrospinal fluid (CSF), showing promise in optimizing therapeutic regimens for various cancers. While CSF has been explored as a source of cfDNA for gliomas, understanding the dynamics of cfDNA abundance and sequencing changes during treatment and recurrence is essential. Leveraging our biobank of longitudinal CSF specimens obtained through CSF access devices, we aimed to determine the potential utility of CSF cfDNA as a monitoring tool for treatment response in glioma patients. Materials and methods: Longitudinal CSF specimens were collected through Ommaya reservoirs (NCT04692337) or ventriculoperitoneal shunts (NCT04692324) from patients with brain tumors, including gliomas. cfDNA was extracted from 1-5 mL of CSF based on available sample volumes and quantified using Qubit. Next-Generation sequencing using PredicineCARE or PredicineSCORE low-pass whole genome sequencing (LPWGS) was performed based on the available cfDNA. Results: CSF collected before versus after resection showed an increase in quantified cfDNA (2.97x, range: 1.58-5.26x), indicating the impact of increased parenchymal disruption and closer contact with CSF. Subsequently, CSF cfDNA decreased during chemoradiation and adjuvant treatment and increased at recurrence, even in patients co-enrolled in immunotherapy trials for IL-7 agonists and pembrolizumab. Notably, copy number burden (CNB) increased at recurrence in three patients with known disease progression and decreased throughout immunotherapy treatment in one patient despite concerns of pseudoprogression. In a patient with a hypermutated glioblastoma, CSF cfDNA revealed over 59 genomic alterations, including MAP2K1, KIT, and PDGFRA. Another patient with a progressing EGFR-amplified GBM showed over 200 new variants in the final sample, with EGFR copy number increasing from 2 to over 30. Conclusion: Analysis of cfDNA throughout a patient’s disease course, encompassing resection and treatment with standard-of-care and experimental therapies, may aid in disease monitoring and treatment response. Further evaluation in a larger patient cohort is needed to determine the sensitivity of changes in mutations, CNB, and cfDNA quantity for glioma disease burden. Citation Format: Riviere-Cazaux Cecile, Xiaoxi Dong, Chao Dai, Wei Mo, Pan Du, Shidong Jia, Terence Burns. Monitoring glioma treatment response through longitudinal analysis of cell-free DNA in cerebrospinal fluid: Insights from a comprehensive study using next-generation sequencing [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 2294.