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Molecular profiling of tumors of the brainstem by sequencing of CSF-derived circulating tumor DNA

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Abstract

Brainstem gliomas are molecularly heterogeneous diseases, many of which are difficult to safely surgically resect and have limited treatment options due to their eloquent location. These constraints pose challenges to biopsy, which limits the use of routine molecular profiling and identification of personalized therapies. Here, we explored the potential of sequencing of circulating tumor DNA (ctDNA) isolated from the cerebrospinal fluid (CSF) of brainstem glioma patients as a less invasive approach for tumor molecular profiling. CSF was obtained from patients either intraoperatively (91.2%, 52/57), from ventricular-peritoneal shunt (3.5%, 2/57), or by lumbar puncture (5.3%, 3/57), all prior to surgical manipulation of the tumor. Deep sequencing of glioma-associated genes was performed on CSF-derived ctDNA and, where available, matched blood and tumor DNA from 57 patients, including nine medullary and 23 diffuse intrinsic pontine gliomas (DIPG). At least one tumor-specific mutation was detected in over 82.5% of CSF ctDNA samples (47/57). In cases with primary tumors harboring at least one mutation, alterations were identified in the CSF ctDNA of 97.3% of cases (36/37). In over 83% (31/37) of cases, all primary tumor alterations were detected in the CSF, and in 91.9% (34/37) of cases, at least half of the alterations were identified. Among ten patients found to have primary tumors negative for mutations, 30% (3/10) had detectable somatic alterations in the CSF. Finally, mutation detection using plasma ctDNA was less sensitive than sequencing the CSF ctDNA (38% vs. 100%, respectively). Our study indicates that deep sequencing of CSF ctDNA is a reliable technique for detecting tumor-specific alterations in brainstem tumors. This approach may offer an alternative approach to stereotactic biopsy for molecular profiling of brainstem tumors.

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Acknowledgements

We thank Lin Qiao and Xuefeng Guo for their help in collecting samples. We would like to thank Honglin Zhu and Yufei Yang for their helpful advices in data analysis. The authors thank Nancy Chu Ji, who was hired to assist in the illustration for Fig. 1, which was inspired by Wang et al. [37].

Funding

Financial support was provided by the National Key Technology Research and Development Program of the Ministry of Science and Technology of China (Grant nos. 2014BAI04B01 and 2015BAI12B04), Beijing Municipal Administration of Hospitals Clinical Medicine Development of Special Funding Support (Grant no. ZYLX201608), and Grant for CP from Beijing Municipal Bureau of Human Resources and Social Security (Grant no. 2017-ZZ-117).

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Author notes

  1. Changcun Pan and Bill H. Diplas contributed equally to this work.

Authors and Affiliations

  1. Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Lu 119, Fengtai District, Beijing, 100070, China

    Changcun Pan, Xin Chen, Yuliang Wu, Xiong Xiao, Yibo Geng, Cheng Xu, Yu Sun, Peng Zhang, Wenhao Wu, Yu Wang, Zhen Wu, Junting Zhang & Liwei Zhang

  2. Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, Durham, NC, USA

    Bill H. Diplas & Hai Yan

  3. Genetron Health (Beijing) Co. Ltd., Beijing, China

    Liping Jiang

  4. State Key Lab of Molecular Oncology, Laboratory of Cell and Molecular Biology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Collaborative Innovation Center for Cancer Medicine, Beijing, China

    Yuchen Jiao

  5. China National Clinical Research Center for Neurological Disease, Nan Si Huan Xi Lu 119, Fengtai District, Beijing, 100070, China

    Liwei Zhang

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  1. Changcun Pan
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Contributions

LZ, HY, and BHD designed the study. CP, XC, YW, XX, YG, PZ, WW, and YW collected the samples, CP, and LJ performed the experiments and collected the data. CP, LJ, YJ, and LZ analyzed the results. CP, LJ, BHD, HY, and LZ wrote the manuscript. CX, YS, ZW, JZ, and YJ, gave conceptual advice.

Corresponding authors

Correspondence to Hai Yan or Liwei Zhang.

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Conflict of interest

HY is a founder of Genetron Health and receives royalties from Personal Genome Diagnostics (PGDX) and Agios. YJ is a co-founder of and Scientific Advisor for Genetron Health. BHD serves as a scientific consultant for Genetron Health.

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401_2018_1936_MOESM7_ESM.tif

Supplementary material 7 Detection of brain tumor-associated alterations in tumor tissue DNA and CSF-derived ctDNA. Comparing the portions of patients with detectable somatic alterations in 47 patients with available matched CSF ctDNA and tumor tissue DNA reveals that the CSF shows similar patterns to tumor DNA across different a tumor types, b tumor locations and c tumor volumes. (TIFF 20275 kb)

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Pan, C., Diplas, B.H., Chen, X. et al. Molecular profiling of tumors of the brainstem by sequencing of CSF-derived circulating tumor DNA. Acta Neuropathol 137, 297–306 (2019). https://doi.org/10.1007/s00401-018-1936-6

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