Department of Chemistry, The University of Chicago, Chicago, IL.
Department of Medicine, The University of Chicago, Chicago, IL.
JCO Precis Oncol. 2024 Oct;8:e2400277. doi: 10.1200/PO.24.00277. Epub 2024 Oct 11.
Using the prostate, lung, colorectal, and ovarian (PLCO) Cancer Screening Trial samples, we identified cell-free DNA (cfDNA) candidate biomarkers bearing the epigenetic mark 5-hydroxymethylcytosine (5hmC) that detected occult colorectal cancer (CRC) up to 36 months before clinical diagnosis.
We performed the 5hmC-seal assay and sequencing on ≤8 ng cfDNA extracted from PLCO study participant plasma samples, including n = 201 cases (diagnosed with CRC within 36 months of blood collection) and n = 401 controls (no cancer diagnosis on follow-up). We conducted association studies and machine learning modeling to analyze the genome-wide 5hmC profiles within training and validation groups that were randomly selected at a 2:1 ratio.
We successfully obtained 5hmC profiles from these decades-old samples. A weighted Cox model of 32 5hmC-modified gene bodies showed a predictive detection value for CRC as early as 36 months before overt tumor diagnosis (training set AUC, 77.1% [95% CI, 72.2 to 81.9] and validation set AUC, 72.8% [95% CI, 65.8 to 79.7]). Notably, the 5hmC-based predictive model showed comparable performance regardless of sex and race/ethnicity, and significantly outperformed risk factors such as age and obesity (assessed as BMI). Finally, when splitting cases at median weighted prediction scores, Kaplan-Meier analyses showed significant risk stratification for CRC occurrence in both the training set (hazard ratio, [HR], 3.3 [95% CI, 2.6 to 5.8]) and validation set (HR, 3.1 [95% CI, 1.8 to 5.8]).
Candidate 5hmC biomarkers and a scoring algorithm have the potential to predict CRC occurrence despite the absence of clinical symptoms and effective predictors. Developing a minimally invasive clinical assay that detects 5hmC-modified biomarkers holds promise for improving early CRC detection and ultimately patient outcomes.
利用前列腺、肺、结直肠和卵巢（PLCO）癌症筛查试验样本，我们鉴定了具有 5-羟甲基胞嘧啶（5hmC）表观遗传标记的无细胞游离 DNA（cfDNA）候选生物标志物，这些标志物能够在临床诊断前 36 个月检测出隐匿性结直肠癌（CRC）。
我们对来自 PLCO 研究参与者血浆样本中提取的≤8ngcfDNA 进行了 5hmC 印迹分析和测序，包括 n=201 例（在采血后 36 个月内诊断为 CRC）和 n=401 例对照（随访期间无癌症诊断）。我们进行了关联研究和机器学习建模，以分析在按 2:1 比例随机选择的训练和验证组中的全基因组 5hmC 图谱。
我们成功地从这些数十年前的样本中获得了 5hmC 图谱。32 个 5hmC 修饰基因体的加权 Cox 模型显示，早在肿瘤诊断前 36 个月就可以对 CRC 进行预测性检测（训练组 AUC，77.1%[95%CI，72.2 至 81.9]和验证组 AUC，72.8%[95%CI，65.8 至 79.7]）。值得注意的是，基于 5hmC 的预测模型无论性别和种族/民族如何，表现都相当，并且显著优于年龄和肥胖等危险因素（评估为 BMI）。最后，当按中位数加权预测评分对病例进行拆分时，生存分析表明，在训练组（风险比 [HR]，3.3[95%CI，2.6 至 5.8]）和验证组（HR，3.1[95%CI，1.8 至 5.8]）中，CRC 发生的风险分层均具有统计学意义。
候选 5hmC 生物标志物和评分算法具有预测 CRC 发生的潜力，尽管没有临床症状和有效的预测指标。开发一种检测 5hmC 修饰生物标志物的微创临床检测方法有望提高早期 CRC 的检测率，并最终改善患者的结局。
