Cerebrospinal fluid derived ctDNA and CTC based molecular analysis highlighting the sampling proximity for clinical significance.

Abstract

e14012 Background: ctDNA based liquid biopsies have transformed cancer care by enabling the detection of actionable mutations, monitoring progression, therapy response, and prognosis. Cerebrospinal (CSF) fluid-based liquid biopsies (CSF-LBx) for CtDNA and CTC may offer a promising alternative, providing critical insights into the molecular landscape of brain metastases. We demonstrate, CSF-LBx with precise detection of ctDNA, having clinically significant markers especially metastasis settings, including leptomeningeal mets. In addition we paired samples having both CSF and blood for ctDNA. Further we captured true single circulating tumor cells (sCTCs), CTCs in paired CSF and in peripheral blood samples. Methods: In a retrospective study, we isolated both ctDNA and CTCs in 11 paired blood and CSF samples having brain metastasis. Patients were presented with, lung with brain and liver mets, multifocal glioblastoma, lobular breast, relapsed cerebellar medulloblastoma, NSCLC, Ca Ovary, lung with medulloblastoma, low grade glioma, etc. Further, CTCs were isolated using OncoDiscover CDSCO India approved platform having anti EpCAM antibody, and sCTCs were captured and released using OncoIndx Ikon platform. Further, OncoIndx comprehensive NGS assay was performed with 1080 genes. Results: In a retrospective we evaluated 11 brain metastatic patients who had paired samples having both CSF and blood. 6 patients had 2 or more sample points. A total of 30 CTCs were isolated from CSF, compared to 42 CTCs isolated from blood. Notably, two CTC clusters were identified in CSF, compared to 10 clusters observed in blood. While ctDNA was isolated from both CSF and blood. NCCN based actionable mutations were identified in 45% (n = 5) of CSF ctDNA samples and 36.36% (n = 4) of blood ctDNA samples. Treatment resistance mutations in the EGFR, ERBB2, PIK3CA, and CDKN2A/2B genes were observed in 4 CSF samples, while sensitive mutations were detected in both CSF and blood. CSF-ctDNA revealed more actionable mutations, including both sensitive and resistance mutations, compared to blood alone in patients in leptomeningeal metastasis. The absence of resistance drivers in blood underscores the importance of sampling more proximally to the metastatic site to improve survival outcomes. Conclusions: CSF has great potential to analyse, both ctDNA and CTC and sCTCs enrichment for molecular profiling. CSF ctDNA exhibited NCCN based actionable mutations, in particular, in cases such as glioblastoma, where tissue biopsies are often not feasible, and blood-based diagnostics face limitations due to DNA sensitivity. Further studies to establish sensitivity and specificity is desired.