Viart Nicolas M, Renault Anne-Laure, Eon-Marchais Séverine, Jiao Yue, Fuhrmann Laetitia, El Houdigui Sophia Murat, Le Gal Dorothée, Cavaciuti Eve, Dondon Marie-Gabrielle, Beauvallet Juana, Raynal Virginie, Stoppa-Lyonnet Dominique, Vincent-Salomon Anne, Andrieu Nadine, Southey Melissa C, Lesueur Fabienne
Inserm, U1331, Institut Curie, PSL University, Mines ParisTech, Paris, France.
Monash University, Clayton, VIC; University of Melbourne, Parkville, VIC, Australia.
Breast Cancer Res. 2025 Mar 11;27(1):36. doi: 10.1186/s13058-025-01988-w.
The ataxia-telangiectasia mutated (ATM) kinase phosphorylates and activates several downstream targets that are essential for DNA damage repair, cell cycle inhibition and apoptosis. Germline biallelic inactivation of the ATM gene causes ataxia-telangiectasia (A-T), and heterozygous pathogenic variant (PV) carriers are at increased risk of cancer, notably breast cancer. This study aimed to investigate whether DNA methylation profiling can be useful as a biomarker to identify tumors arising in ATM PV carriers, which may help for the management and optimal tailoring of therapies of these patients.
Breast tumor enriched DNA was prepared from 2 A-T patients, 27 patients carrying an ATM PV, 6 patients carrying a variant of uncertain clinical significance and 484 noncarriers enrolled in epidemiological studies conducted in France and Australia to investigate genetic and nongenetic factors involved in breast cancer susceptibility. Genome-wide DNA methylation analysis was performed using the Illumina Infinium HumanMethylation EPIC and 450K BeadChips. Correlation between promoter methylation and gene expression was assessed for 10 tumors for which transcriptomic data were available.
We found that the ATM promoter was hypermethylated in 62% of tumors of heterozygous PV carriers compared to the mean methylation level of ATM promoter in tumors of noncarriers. Gene set enrichment analyses identified 47 biological pathways enriched in hypermethylated genes involved in neoplastic, neurodegenerative and metabolic-related pathways in tumor of PV carriers. Among the 327 differentially methylated promoters, promoters of ARHGAP40, SCGB3A1 (HIN-1), and CYBRD1 (DCYTB) were hypermethylated and associated with a lower gene expression in these tumors. Moreover, using three different deep learning algorithms (logistic regression, random forest and XGBoost), we identified a set of 27 additional biomarkers predictive of ATM status, which could be used in the future to provide evidence for or against pathogenicity in ATM variant classification strategies.
We showed that breast tumors that arise in women who carry an ATM PV display a specific genome-wide DNA methylation profile. Specifically, the methylation pattern of 27 key gene promoters was predictive of ATM PV status of the women. These genes may also represent new medical prevention and therapeutic targets for these women.
共济失调毛细血管扩张症突变（ATM）激酶可磷酸化并激活多个对DNA损伤修复、细胞周期抑制和细胞凋亡至关重要的下游靶点。ATM基因的种系双等位基因失活会导致共济失调毛细血管扩张症（A-T），杂合致病性变异（PV）携带者患癌症的风险增加，尤其是乳腺癌。本研究旨在调查DNA甲基化谱是否可用作生物标志物，以识别ATM PV携带者中发生的肿瘤，这可能有助于这些患者的治疗管理和优化治疗方案。
从2例A-T患者、27例携带ATM PV的患者、6例携带临床意义不确定变异的患者以及484例未携带者中提取富含乳腺肿瘤的DNA，这些患者参与了在法国和澳大利亚进行的流行病学研究，以调查乳腺癌易感性的遗传和非遗传因素。使用Illumina Infinium HumanMethylation EPIC和450K BeadChips进行全基因组DNA甲基化分析。对10个有转录组数据的肿瘤评估启动子甲基化与基因表达之间的相关性。
我们发现，与非携带者肿瘤中ATM启动子的平均甲基化水平相比，杂合PV携带者肿瘤中62%的ATM启动子发生了高甲基化。基因集富集分析确定了47条生物途径，这些途径在PV携带者肿瘤中与肿瘤、神经退行性和代谢相关途径中高甲基化基因富集。在327个差异甲基化启动子中，ARHGAP40、SCGB3A1（HIN-1）和CYBRD1（DCYTB）的启动子发生了高甲基化，并与这些肿瘤中较低的基因表达相关。此外，使用三种不同的深度学习算法（逻辑回归、随机森林和XGBoost），我们确定了一组另外27个预测ATM状态的生物标志物，未来可用于为ATM变异分类策略中的致病性提供支持或反对的证据。
我们表明，携带ATM PV的女性发生的乳腺肿瘤表现出特定的全基因组DNA甲基化谱。具体而言，27个关键基因启动子的甲基化模式可预测女性的ATM PV状态。这些基因也可能代表这些女性新的医学预防和治疗靶点。
