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On J, Natsumeda M, Takahashi H, Koyama A, Shibuma S, Shibata N, Watanabe J, Saito S, Kanemaru Y, Tsukamoto Y, Okada M, Ogura R, Eda T, Tada M, Shimizu H, Adachi JI, Mishima K, Nishikawa R, Kakita A, Oishi M. Reliable detection of genetic alterations in cyst fluid DNA for the diagnosis of brain tumors. J Neurooncol 2024; 166:273-282. [PMID: 38227143 DOI: 10.1007/s11060-023-04555-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/26/2023] [Indexed: 01/17/2024]
Abstract
PURPOSE Liquid biopsy of cyst fluid in brain tumors has not been extensively studied to date. The present study was performed to see whether diagnostic genetic alterations found in brain tumor tissue DNA could also be detected in cell-free DNA (cfDNA) of cyst fluid in cystic brain tumors. METHODS Cyst fluid was obtained from 22 patients undergoing surgery for a cystic brain tumor with confirmed genetic alterations in tumor DNA. Pathological diagnoses based on WHO 2021 classification and diagnostic alterations in the tumor DNA, such as IDH1 R132H and TERT promoter mutation for oligodendrogliomas, were detected by Sanger sequencing. The same alterations were analyzed by both droplet digital PCR (ddPCR) and Sanger sequencing in cyst fluid cfDNA. Additionally, multiplex ligation-dependent probe amplification (MLPA) assays were performed to assess 1p/19q status, presence of CDKN2A loss, PTEN loss and EGFR amplification, to assess whether differentiating between astrocytomas and oligodendrogliomas and grading is possible from cyst fluid cfDNA. RESULTS Twenty-five genetic alterations were found in 22 tumor samples. All (100%) alterations were detected in cyst fluid cfDNA by ddPCR. Twenty of the 25 (80%) alterations were also detected by Sanger sequencing of cyst fluid cfDNA. Variant allele frequency (VAF) in cyst fluid cfDNA was comparable to that of tumor DNA (R = 0.62, Pearson's correlation). MLPA was feasible in 11 out of 17 (65%) diffuse gliomas, with close correlation of results between tumor DNA and cyst fluid cfDNA. CONCLUSION Cell-free DNA obtained from cyst fluid in cystic brain tumors is a reliable alternative to tumor DNA when diagnosing brain tumors.
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Affiliation(s)
- Jotaro On
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Manabu Natsumeda
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan.
- Advanced Treatment of Neurological Diseases Branch, Brain Research Institute, Niigata University, Niigata, Japan.
| | - Haruhiko Takahashi
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akihide Koyama
- Department of Legal Medicine, Niigata University Graduate School of Medical and Dental Science, Niigata, Japan
| | - Satoshi Shibuma
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Nao Shibata
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jun Watanabe
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Shoji Saito
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yu Kanemaru
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yoshihiro Tsukamoto
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masayasu Okada
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Ryosuke Ogura
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Takeyoshi Eda
- Division of Pharmacy, Medical and Dental Hospital, Niigata University, Niigata, Japan
| | - Mari Tada
- Department of Pathology, Brain Research Institute, Niigata, Japan
| | - Hiroshi Shimizu
- Department of Pathology, Brain Research Institute, Niigata, Japan
| | - Jun-Ichi Adachi
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Kazuhiko Mishima
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Ryo Nishikawa
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata, Japan
| | - Makoto Oishi
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
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