BIOM-05 CHARACTERIZATION OF TUMOR-DERIVED DNA MUTATIONS, COPY NUMBER CHANGES, AND METHYLATED FRAGMENTS WITHIN CEREBROSPINAL FLUID AND PLASMA FROM PATIENTS UNDERGOING SURGERY FOR LUNG CANCER BRAIN METASTASIS

Abstract Surgical management of brain metastasis (BrM) improves outcomes in selected patients, yet predicting CNS progression following surgery remains challenging. To identify circulating tumor-(ct)DNA markers associated with disease progression, we collected patient-matched BrM tissue, cerebrospinal fluid (CSF), and/or plasma from 75 patients undergoing lung cancer BrM resection. CSF and plasma were also collected from patients who progressed to leptomeningeal disease (LMD). Cell-free DNA was extractable (>1ng) in 76% of CSF (38/50) and 100% of plasma samples (78/78). We assessed mutations by tissue-informed ultradeep sequencing via the PredicineBEACONTM MRD assay as well as genome-wide copy number variants (CNV) and differentially methylated fragments (DMFs) via the PredicineEPICTM DNA methylation assay. In patients undergoing craniotomy for non-small cell lung cancer, we identified ctDNA mutations, CNVs, and DMFs in 100%, 83%, and 100% of CSF and 79%, 23%, and 100% of plasma, respectively. In matched CSF:plasma pairs, all CSF mutant (p=.019) and CNV (p=.02) tumor fractions and 76% of CSF DMF counts were higher than plasma. Only 22% of CSF DMFs were concordant with matched plasma and 37% of the plasma DMFs were concordant with matched CSF, suggesting ctDNA methylation in the CNS may be related but distinct from the periphery. CSF shared 74% DMF concordance with matched BrM tissue whereas plasma shared 50%. Overall survival correlated with plasma mutant ctDNA (tumor fractions of >1% vs. <1% = HR: 2.2, CI: 1.1-4.4, p=.025) and DMFs (counts >5000 vs. <500= HR: 20.7, CI: 3.8 to 113, p=.0005), yet CSF ctDNA levels did not correlate with outcome. However, the number of unique DMF sites detected in CSF increased in patients with LMD versus parenchymal BrM (2716 vs. 442, p=.007). Furthermore, DMF counts were higher in lung adenocarcinoma BrMs that later progressed to LMD (p=.002), suggesting aberrant methylation may contribute to BrM-to-LMD progression.