Dynamic monitoring of cerebrospinal fluid circulating tumor DNA to identify unique genetic profiles of brain metastatic tumors and better predict intracranial tumor responses in non-small cell lung cancer patients with brain metastases: a prospective cohort study (GASTO 1028)

• Published in: BMC medicine 2022-11, Vol.20 (1), p.398-12, Article 398
• Main Authors: Li, Meichen, Chen, Jing, Zhang, Baishen, Yu, Juan, Wang, Na, Li, Delan, Shao, Yang, Zhu, Dongqin, Liang, Chuqiao, Ma, Yutong, Ou, Qiuxiang, Hou, Xue, Chen, Likun
• Format: Article
• Language: English
• Subjects: Biological markers; Biomarkers, Tumor - analysis; Biomarkers, Tumor - genetics; Biopsy; Blood-brain barrier; Brain - pathology; Brain cancer; Brain metastases; Brain Neoplasms - diagnosis; Brain Neoplasms - genetics; Brain tumors; Cancer; Cancer therapies; Carcinoma, Non-Small-Cell Lung - diagnosis; Carcinoma, Non-Small-Cell Lung - genetics; Care and treatment; Central nervous system; Cerebrospinal fluid; Circulating tumor DNA; Circulating Tumor DNA - genetics; Clonal evolution; Cohort analysis; Copy number; Deoxyribonucleic acid; Diagnosis; Diagnostic tests; DNA; DNA Copy Number Variations; Evolution; Extrachromosomal DNA; Genes; Genetic aspects; Genetic Profile; Genomes; Health aspects; Heterogeneity; Humans; Intracranial response; Lung cancer; Lung cancer, Non-small cell; Lung Neoplasms - diagnosis; Lung Neoplasms - genetics; Lung Neoplasms - pathology; Metastases; Metastasis; Mutation; Next-generation sequencing; Non-small cell lung carcinoma; Oncology, Experimental; Patients; Plasma; Prognosis; Prospective Studies; Puncture; Reduction; Small cell lung carcinoma; Software; Spine; Testing laboratories; Tumors
• ISSN: 1741-7015; 1741-7015
• DOI: 10.1186/s12916-022-02595-8

Due to the blood-brain barrier, plasma is not an ideal source to evaluate the genetic characteristics of central nervous system tumors. Thus, cerebrospinal fluid (CSF) is becoming an alternative biopsy type to evaluate the genetic landscape of intracranial tumors. We aimed to explore the genetic profiles of CSF-derived circulating tumor DNA (ctDNA) to predict intracranial tumor responses and monitor mutational evolution during the treatment of non-small cell lung cancer (NSCLC) patients with brain metastases. We conducted a prospective study of 92 newly diagnosed NSCLC patients with brain metastases. Paired CSF and plasma samples were collected at baseline, 8 weeks after treatment initiation, and disease progression. All samples underwent next-generation sequencing of 425 cancer-related genes. At baseline, the positive detection rates of ctDNA in CSF, plasma, and extracranial tumors were 63.7% (58/91), 91.1% (82/90), and 100% (58/58), respectively. A high level of genetic heterogeneity was observed between paired CSF and plasma, while concordance in driver mutations was also observed. A higher number of unique copy number variations was detected in CSF-ctDNA than in plasma. ctDNA positivity of CSF samples at baseline was associated with poor outcomes (HR=2.565, P=0.003). Moreover, patients with ≥ 50% reductions in the concentrations of CSF ctDNA after 8 weeks of treatment had significantly longer intracranial progression-free survivals (PFS) than patients with < 50% reductions in CSF ctDNA concentrations (13.27 months vs 6.13 months, HR=0.308, P=0.017). A ≥ 50% reduction in CSF ctDNA concentrations had better concordance with radiographic intracranial tumor responses than plasma. A ≥ 50% reduction in plasma ctDNA concentrations was also associated with longer extracranial PFS (11.57 months vs 6.20 months, HR=0.406, P=0.033). Based on clonal evolution analyses, the accumulation of subclonal mutations in CSF ctDNA was observed after 8 weeks of treatment. The clonal mutations that remained in more than 80% in CSF after 8 weeks also predicted shorter intracranial PFS (HR=3.785, P=0.039). CSF ctDNA exhibited unique genetic profiles of brain metastases, and dynamic changes in CSF ctDNA could better predict intracranial tumor responses and track clonal evolution during treatment in NSCLC patients with brain metastases. ClinicalTrials.gov identifier: NCT03257735.