Evaluating the Cerebrospinal Fluid ctDNA detection by Next-Generation Sequencing in the diagnosis of Meningeal Carcinomatosis

Abstract

Background Meningeal carcinomatosis (MC) is the most severe form of brain metastasis and causes significant morbidity and mortality. Currently, the diagnosis of MC is routinely confirmed on the basis of clinical signs and symptoms, positive cerebrospinal fluid (CSF) cytology, and/or neuroimaging (contrast-enhanced brain MRI and/or CT) features. However, negative rate of CSF cytology and neuroimaging findings often result in a failure to diagnose MC from the patients who actually have the disease. Methods A total of 35 CSF samples were collected from 35 patients with MC for CSF cytology examination, CSF tumor-derived circulating tumor DNA (ctDNA) extraction and cancer-associated gene mutations detection by next-generation sequencing (NGS) at the same time. Results The most frequent primary tumor in this study was lung cancer (26/35, 74.29%), followed by gastric cancer (2/35, 5.71%), breast cancer (2/35, 5.71%), prostatic cancer (1/35, 2.86%), parotid gland carcinoma (1/35, 2.86%) and lymphoma (1/35, 2.86%) while no primary tumor could be found in the remaining 2 patients in spite of using various inspection methods. Twenty-five CSF samples (25/35; 71.43%) were found neoplastic cells in CSF cytology examination while all of the 35 CSF samples (35/35; 100%) were revealed having detectable ctDNA in which cancer-associated gene mutations were detected. All of 35 patients with MC in the study underwent contrast-enhanced brain MRI and/or CT and 22 neuroimaging features (22/35; 62.86%) were consistent with MC. The sensitivity of the neuroimaging was 88.00% (95% confidence intervals [95% CI], 75.26 to 100) (p=22/25) and 62.86% (95% CI, 46.85 to 78.87) (p=22/35) compared to those of CSF cytology and CSF ctDNA, respectively. The sensitivity of the CSF cytology was 71.43% (95% CI, 56.46 to 86.40) (n=25/35) compared to that of CSF ctDNA. Conclusions This study suggests a higher sensitivity of CSF ctDNA than those of CSF cytology and neuroimaging findings. The utilizing CSF ctDNA as liquid biopsy technology for the diagnosis of MC based on the detection of cancer-associated gene mutations in ctDNA from CSF offers an alternative and DNA-based test for the diagnosis of MC, especially for cases with persistently negative CSF cytology and/or negative neuroimaging findings.

Circulating tumour DNA — looking beyond the blood

“…The ctDNA detection rate and VAFs of detected alleles were both higher in CSF samples than in plasma (sensitivity 81.5% and 62.5% for CSF and plasma, respectively). The maximum allelic fraction was 43.6% for CSF versus 4.6% for plasma and a unique genomic profile was observed in the CSF, primarily owing to the presence of CSF-specific copy number variants 20,88,90 . In patients with NSCLC, analysis of CSF ctDNA might enable more sensitive detection of alterations than analysis of plasma given that EGFR alterations are typically detected at a sensitivity of 70-90% in plasma samples from patients with advanced-stage EGFR-mutant disease [91][92][93][94][95] .…”

Cerebrospinal fluid as a medium of liquid biopsy in the management of patients with non-small-cell lung cancer having central nervous system metastasis

“…On the other hand, cell-free DNA extracted from CSF of patients with cancer is thought to be enriched for ctDNA due to the significantly lower number of normal cells in CSF compared with that in blood. Using [17,20,[36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53]). Most studies have focused on patients with EGFR-mutant NSCLC with LM due to the relatively high number of these patients [10].…”

“…mutation allele-specific amplification, Swinkels et al[36] first identified KRAS mutation in CSF of two patients with NSCLC with LM. Subsequent studies, using either polymerase chain reaction (PCR) or NGS, have demonstrated that CSF ctDNA is a feasible material for mutation detection, particularly in patients with LM, with a detection rate as high as 100%[17,[37][38][39][40][41][42][43][44][45][46][47][48][49][50]. Published studies on ctDNA in CSF of patients with NSCLC with CNS metastasis are summarized in Table2(Ref.…”