PO.CL01.09 · 临床研究
短双链cfDNA：一类用于癌症诊断的新型精准生物标志物
Short double-stranded cfDNA: A novel precision biomarker class for cancer diagnostics
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
背景：癌症诊断依赖高度特异且灵敏的生物标志物，以检测癌症进展的早期阶段以及疾病复发（MRD）。然而，当前方法往往无法满足这些需求，而基于游离DNA（cfDNA），尤其是短双链游离DNA（足迹DNA，footprint DNA）的液体活检为改进带来巨大希望。足迹DNA源自包括转录因子在内的调控蛋白在DNA结合基序处的相互作用，包含来自血浆样本的全基因组DNA足迹。对足迹DNA进行选择性富集和定量分析，可揭示用于复杂疾病诊断（包括多种癌症类型）的显著不同的特征。
方法：通过高通量测序分析了来自多种肿瘤类型（包括结直肠癌和胰腺导管腺癌）以及非癌症对照的200余份血浆样本的足迹DNA，随后进行生物信息学峰识别，以生成全基因组液体足迹位点的全面参考注释。此外，还使用对个体患者样本足迹DNA的定量评估来区分临床状态，并与标准诊疗进行基准比较。
结果：峰识别（peak calling）揭示在约650万个足迹区域中存在约860万个不同的峰。330万个峰与已注释的转录因子结合位点（TFBS）重叠。此外，33,675个启动子区域、55,406个CTCF位点以及超过100,000个增强子结合区域被足迹DNA信号覆盖。我们还发现，特定基因组位点的足迹DNA与来自肝脏或肾脏等主要器官系统的生理标志物（如ALT或尿素）呈半定量相关。在一个概念验证队列中，差异性足迹DNA生物标志物能够区分临床状态，尤其还能区分密切相关的癌症类型——结直肠癌和胰腺导管腺癌（PDAC）。即便是同一器官疾病（SOD），如胰腺炎和PDAC，也能使用足迹DNA生物标志物加以特异性区分。
结论：足迹DNA在癌症诊断方面具有强大潜力，这已通过疾病与癌症的区分以及同一器官疾病之间的区分得到证明。足迹DNA富集为鉴别性足迹DNA生物标志物的鉴定平台奠定了基础，从而实现用于临床应用的基于panel的癌症检测。这为早期癌症检测和微小残留病（MRD）监测开辟了新的可能性。因此，全面的足迹注释将为癌症及其他复杂疾病的诊断提供坚实基础。
查看英文原文 English abstract
Background: Cancer diagnostics relies on highly specific and sensitive biomarkers to detect early stages in cancer progression as well as recurrence of disease (MRD). However, current approaches often fail to fulfill these needs, however, liquid biopsy based on cell-free DNA (cfDNA) and in particular short double-stranded cell-free DNA (footprint DNA) holds great promise for improvements. Derived from interaction of regulatory proteins including transcription factors at DNA-binding motifs, footprint DNA comprises genome-wide DNA footprints from plasma samples. Selective enrichment and quantitative analyses of footprint DNA reveal significantly different signatures for complex diseases diagnostics including various cancer types.
Methods: Footprint DNA of more than 200 plasma samples from various tumor types, including colorectal cancer and pancreatic ductal adenocarcinoma, as well as non-cancer controls were analyzed by high-throughput sequencing followed by bioinformatic peak identifications to generate a comprehensive reference annotation for genome-wide liquid footprint sites. Additionally, quantitative evaluation of footprint DNA from individual patient samples was used to differentiate between clinical conditions and benchmarking against standard of care diagnostics.
Results: Peak calling revealed approximately 8.6 million different peaks in about 6.5 million footprint regions. 3.3 million peaks overlap with annotated transcription factor bindings sites (TFBS). Moreover, 33,675 promotor regions, 55,406 CTCF sites and more than 100,000 enhancer binding regions are covered by footprint DNA signals. We also found that footprint DNA at defined genomic loci semi-quantitatively correlated with physiological markers like ALT or urea from major organ systems including liver or kidney. In a proof-of-concept cohort, differential footprint DNA biomarkers distinguished between clinical conditions, notably also closely related cancer types of colorectal cancer and pancreatic ductal adenocarcinoma (PDAC). Even same organ diseases (SOD) like pancreatitis and PDAC could be specifically discriminated using footprint DNA biomarkers.
Conclusion: Footprint DNA bears strong potential for cancer diagnostics, demonstrated by disease and cancer discrimination as well as differentiation between same organ disease. Footprint DNA enrichment sets the groundwork as identification platform of discriminatory footprint DNA biomarkers, which allows panel-based cancer detection for clinical applications. This opens new possibilities in early cancer detection and monitoring of minimal residual disease (MRD). Comprehensive footprint annotation will therefore provide a strong basis for the diagnostic of cancer and other complex diseases.
利益披露 Disclosure
M. Sonntag, None..
Z. Zhang, None..
D. Leupold, None.
J. Mueller,
Hopp Children's cancer center Heidelberg Employment.
Y. Vainshtein, None..
C. Hartwig, None..
G. F. Weber, None.
K. Sohn,
Noscendo GmbH Patent.