When Blood Can’t See It: CSF Can
For patients with EGFR-mutant non-small cell lung cancer (NSCLC) who develop leptomeningeal metastases, the blood-brain barrier isn’t just a clinical obstacle, it’s a diagnostic one. Circulating tumour DNA shed by CNS lesions often fails to cross into peripheral blood, leaving conventional liquid biopsy blind to the very drivers causing the most devastating disease progression.
This case report demonstrates how cerebrospinal fluid (CSF)-based NGS sequencing, combined with live single circulating tumour cell (sCTC) isolation, can reveal what blood alone cannot, and change the course of treatment.
The Patient
A 64-year-old non-smoking female presented in December 2020 with metastatic EGFR-mutant lung adenocarcinoma harbouring an EGFR Exon 19 deletion. She was started on Osimertinib per FLAURA trial guidelines and achieved a complete metabolic response lasting nearly two years.
After disease progression and several treatment modifications; including SBRT, gefitinib, and a platinum doublet, she developed leptomeningeal disease in May 2024. Blood-based liquid biopsy at this point showed no actionable information. CSF profiling was the only path forward.
What CSF Sequencing Revealed
Using 1Cell.ai’s OncoIncytes™ platform for live sCTC isolation and OncoIndx® 1080-gene panel for comprehensive genomic profiling, CSF analysis uncovered a dual-driver profile invisible in plasma:
EGFR Exon 19 deletion at 92% variant allele fraction, confirming continued EGFR dependency in the CNS compartment
ERBB2 amplification at 21 copies; a bypass resistance mechanism entirely absent in matched blood samples
TP53 co-mutations further characterising the tumour’s evolving genomic landscape
These findings directly guided a combination therapy strategy: osimertinib continued for systemic EGFR control, combined with intrathecal trastuzumab targeting the ERBB2 amplification driving leptomeningeal spread. Within weeks, clinical improvement followed:
“And July 2024 MRI confirmed resolution of leptomeningeal enhancement.”
Longitudinal Molecular Tracking
This case demonstrates the power of serial, multi-modal liquid biopsy across four timepoints spanning over four years of disease evolution. At each inflection point: initial diagnosis, osimertinib resistance, ERBB2-driven leptomeningeal spread, and post-treatment stabilisation; molecular profiling directly shaped the treatment decision.
Critically, as leptomeningeal disease came under control, ctDNA and CTCs reappeared in blood while disappearing from CSF, confirming the site-specific biology of tumour DNA shedding, and the importance of sampling proximally to the disease site.
Why This Matters
This case establishes a framework for CSF-based liquid biopsy in CNS metastatic NSCLC, demonstrating that:
CSF profiling can identify dual actionable drivers that remain entirely undetectable in plasma
Intrathecal therapy guided by CSF genomics can achieve durable leptomeningeal control even in complex, multi-driver disease.
Sequential molecular profiling, not single-timepoint testing, is essential for managing evolving resistance in oncogene-driven NSCLC
Almost 1.5 years after leptomeningeal diagnosis and 5 years after initial presentation, the patient continues to do well, a testament to what precision oncology, guided by the right liquid biopsy at the right site, can achieve.
Published in The Journal of Liquid Biopsy, 2025| JLB 10 (2025) 100332 | DOI: 10.1016/j.jlb.2025.100332