NGS to reveal heterogeneity between cerebrospinal fluid and plasma ctDNA among non-small cell lung cancer patients with leptomeningeal carcinomatosis.

Abstract

9022 Background: In current clinical setting, NSCLC patients harboring specific driver mutation were usually treated guiding by prior profiling of the primary tumor when developed to brain metastasis. Some studies have shown that circulating tumor DNA (ctDNA) derived from cerebrospinal fluid (CSF) can reveal unique genomic alterations present in brain malignancies. We assessed CSF as a liquid biopsy media and compared to matched plasma. Methods: We performed capture-based ultra deep sequencing on ctDNA derived from matched CSF, plasma of 40 non-small cell lung cancer (NSCLC) patients with suspected leptomeningeal carcinomatosis (LC) using a panel consisting of 168 genes. Results: Among the 40 suspected LC cases, 35 were confirmed to have LC, ctDNA in CSF from the 5 non-LC cases are all undetectable. Circulating tumor DNA was detected in 93.8% of CSF and 66.7% of plasma. We compared mutation profiles and identified 86 and 46 SNVs from CSF and plasma, respectively, with 42 SNVs overlapping. Furthermore, ctDNA from CSF revealed many copy number variations (CNVs) that were not detected from plasma (189 CNVs vs. 3 CNVs). The average maximum allelic fraction (AF) of CSF ctDNA is significantly higher than in plasma (56.7% vs. 4.4% p < 10^-6). Twenty-eight patients were pre-treated with EGFR-TKIs and developed subsequent resistance. EGFR T790M and MET amplification were detected in 21% and 39% in CSF, respectively, showing a unique resistance profile among leptomeningeal metastases patients compared to the general population. Interestingly, 60% of CSF samples harbor TP53 loss of heterozygosity, only 11% of which were detected in the matched plasma samples. Such heterogeneity may reflect unique biological themes for brain metastatic tumor sub-clones. Furthermore, 26 patients received molecular targeted therapy based on the results from CSF, and 23 reported alleviation of symptoms at subsequent evaluations. Conclusions: Collectively, our data reveal that ctDNA derived from CSF provides a unique and more comprehensive characterization of genomic alterations of leptomeningeal carcinomatosis than plasma, supporting the importance of CSF as a liquid biopsy media.

Advanced Lung Adenocarcinoma Patient with ERBB2 Amplification Identified by Comprehensive Genomic Profiling Benefits from Trastuzumab

“…It would also have been interesting to evaluate whether the brain lesions differed from the lung lesion in the genetic actionability profile. In this regard, genetic testing of cerebrospinal fluid could have been considered [25].…”

Cerebrospinal fluid cell-free tumour DNA as a liquid biopsy for primary brain tumours and central nervous system metastases

“…Analysis of CSF ctDNA has also shown gene mutations associated with therapy resistance [15,27,64]. Drug-resistance mutations in patients whose CNS disease progressed during TKI therapy (EGFR, ALK, HER2, or BRAF) were identified in CSF ctDNA in one-third of cases [27].…”

“…In metastatic melanoma spreading to the leptomeninges, CSF examination using PCR-based techniques has been successfully used for diagnosis and monitoring response to therapy based on the detection of driver mutations, e.g. affecting BRAF [64,75].…”

“…Recent and ongoing studies address the role of CSF ctDNA in patients with EGFR-mutant NSCLC and leptomeningeal metastasis [27,64]. Forty NSCLC patients with suspected leptomeningeal metastasis were profiled, including 35 patients with a confirmed leptomeningeal metastases [64]. EGFR T790M and MET amplification were detected in 21% and 39% in CSF ctDNA, respectively, suggesting a resistance profile to EGFR-TKI associated with leptomeningeal disease.…”

Leptomeningeal metastases from non-small cell lung cancer: state of the art and recent advances

“…Moreover, the T790M mutation has not been identified neither in BM or LM [44,45] , nor in CSF of patients who have developed LM following EGFR TKIs [46] . Jiang et al [47] reported a lower frequency of T790M mutation (21%) and a higher frequency of MET amplification (39%) in the CSF, suggesting that MET amplification could confer a major risk of leptomeningeal invasion [48] .…”