基于纳米孔的肺癌脑转移患者脑脊液中游离DNA片段化和甲基化图谱

Nanopore-based cell-free DNA fragmentation and methylation profiles from the cerebral spinal fluid of patients with lung cancer brain metastases.

作者信息

Chen Tianqi, Bai Xiangqi, Burnside Georgiana, Trinh Thy Trang Hoang, Gephart Melanie Hayden, Lau Billy T, Ji Hanlee P

机构信息

Division of Oncology, Department of Medicine, Stanford University, School of medicine, Stanford, CA, 94305, United States.

Department of Neurosurgery, Stanford University, Stanford, CA, 94305, United States.

出版信息

bioRxiv. 2025 Jul 31:2025.07.28.667300. doi: 10.1101/2025.07.28.667300.

DOI:10.1101/2025.07.28.667300

PMID:40766439

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12324296/

Abstract

BACKGROUND

Non-small cell lung cancer () patients with brain metastases () have a poor prognosis. Cerebrospinal fluid () is a source of cell free DNA () from the brain and its methylation and fragmentation properties may be an indicator of NSCLC-BMET.

METHODS

We applied a nanopore single-molecule sequencing approach to characterize the fragmentation, methylation and hydroxymethylation patterns present in CSF-derived cfDNA from NSCLC-BMET patients (N=15). We compared the cancer cfDNA finding to non-cancer healthy controls (N=11) and their CSF cfDNA. We also compared the fragmentation patterns between CSF-derived cfDNA and plasma-derived cfDNA.

RESULTS

We observed enriched mono-nucleosome levels and significantly higher mono-/trinucleosome ratios in cancer patients. Comparison with plasma-derived cfDNA further confirmed the unique fragmentation features of CSF-derived cfDNA. Distinct methylation and hydroxymethylation patterns were observed between cancer and control CSF samples. We observed significantly lower degree of hydroxymethylation in cancer patients compared to healthy controls and the affected genes had different pathway profiles.

CONCLUSIONS

CSF cfDNA in patients with NSCLC-BMET had a distinct profiles of DNA fragmentation, methylation and hydroxymethylation.

摘要

背景

伴有脑转移（BMET）的非小细胞肺癌（NSCLC）患者预后较差。脑脊液（CSF）是大脑游离DNA（cfDNA）的一个来源，其甲基化和片段化特性可能是NSCLC-BMET的一个指标。

方法

我们应用纳米孔单分子测序方法来表征NSCLC-BMET患者（N = 15）脑脊液来源的cfDNA中存在的片段化、甲基化和羟甲基化模式。我们将癌症cfDNA的发现结果与非癌症健康对照（N = 11）及其脑脊液cfDNA进行了比较。我们还比较了脑脊液来源的cfDNA和血浆来源的cfDNA之间的片段化模式。

结果

我们在癌症患者中观察到单核小体水平升高以及单核小体/三核小体比率显著更高。与血浆来源的cfDNA比较进一步证实了脑脊液来源的cfDNA独特的片段化特征。在癌症和对照脑脊液样本之间观察到了不同的甲基化和羟甲基化模式。与健康对照相比，我们在癌症患者中观察到羟甲基化程度显著更低，并且受影响的基因具有不同的通路谱。