Cerebrospinal fluid ctDNA clarifies clonal divergence: leptomeningeal flare of EGFR-mutant disease after switch to selpercatinib for acquired RET fusion

Liquid biopsy can expose spatially segregated resistance biology that is invisible to single-site tissue testing, particularly across the blood-brain barrier. We report how cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) clarified therapeutic direction in <i>EGFR</i>-mutated non-small-cell lung cancer (NSCLC) with leptomeningeal involvement. A 67-year-old woman with <i>EGFR</i> exon 19-deleted adenocarcinoma received afatinib followed by long-term osimertinib. After three years, progression of the primary lesion prompted rebiopsy, which revealed a <i>CCDC6-RET</i> fusion with strong RET immunoreactivity. Selpercatinib monotherapy yielded minor thoracic shrinkage at 1 month but was followed by dizziness and MRI evidence of leptomeningeal enhancement at 3 months. CSF analysis showed pleocytosis without malignant cells. Critically, CSF ctDNA demonstrated the <i>EGFR</i> E746_A750 deletion at 29.2 % variant allele frequency by amplicon sequencing, whereas the <i>CCDC6-RET</i> fusion was undetectable by targeted sequencing and highly sensitive single-plex qPCR using junction-specific primers. Re-challenging with osimertinib rapidly improved symptoms and led to resolution of leptomeningeal enhancement. These data indicate clonal divergence at acquired resistance: a <i>RET</i>-fusion clone dominated the thoracic compartment while <i>EGFR</i>-addicted clones predominated in the leptomeninges. The leptomeningeal flare after discontinuing EGFR inhibition highlights the risk of switching to RET inhibitor monotherapy when CNS disease is driven by the original <i>EGFR</i> mutant clone. CSF liquid biopsy provided actionable, compartment-specific genotyping that outperformed cytology and guided effective retreatment. Incorporating CSF ctDNA into routine evaluation may improve therapeutic alignment across sanctuary sites; when feasible, maintaining EGFR blockade should be considered when CNS involvement is suspected in <i>EGFR</i>-mutated NSCLC in routine practice.