PO.MCB06.02 · 分子与细胞生物学
携带嵌合染色体改变的白细胞克隆性扩增加速表观遗传衰老并重塑局部DNA甲基化
Clonal expansion of leukocytes harboring mosaic chromosomal alterations accelerates epigenetic aging and reshapes local DNA methylation
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
嵌合染色体改变（mCAs）是一种年龄相关性克隆性造血，源于造血细胞中合子后的染色体获得、丢失或拷贝数中性杂合性缺失（CN-LOH）。DNA甲基化可作为生物学衰老的分子度量指标，并可通过基于甲基化的表观遗传时钟进行量化。mCAs在多大程度上加速表观遗传衰老或诱导局部甲基化重塑尚不明确。
我们分析了前列腺、肺、结直肠和卵巢（PLCO）癌症筛查试验中482名无癌参与者，采样时年龄54-77岁。选择基于mCA状态（mCA携带者=261）、既往基因分型、充足的DNA以及年龄和性别。Illumina MethylationEPIC芯片数据的原始IDAT文件使用ChAMP流程处理，采用BMIQ标准化和ComBat批次校正。使用dnaMethyAge R包实施六种既有的甲基化时钟（Horvath2013和2018、Hannum、PhenoAge、GrimAge和DunedinPACE）以计算基于残差的年龄加速。多变量线性模型校正年龄、性别、血统、吸烟和BMI，将mCA携带者与无mCA个体进行比较，同时比较常染色体、mLOY、mLOX和多重mCA亚型。使用EpiDISH结合IDOL优化的FlowSorted.BloodExtended.EPIC参考估算免疫细胞组成。为鉴定局部甲基化效应，采用普通最小二乘回归检验mCA受累区域内每个CpG的beta值以进行差异甲基化分析，并使用Ingenuity通路分析（IPA）进行功能富集。
在六种表观遗传时钟中，mCA携带者相比无mCA者表现出更高的表观遗传年龄加速（例如PhenoAge beta=3.46，95% CI 1.670-5.22，p=1.32×10^-4），其中常染色体mCA的效应量最大。全血的甲基化解卷积揭示白细胞组成发生改变，包括携带多重mCA的参与者中记忆B细胞比例升高、CD4记忆细胞比例降低（B细胞：beta=0.024，p=2.0×10^-8；CD4：beta=-0.017，p=0.017）。对mCA区域内每个CpG位点甲基化水平的分析鉴定出2,553个显著探针（1,973个低甲基化，580个高甲基化），在多个CN-LOH和获得区域可见显著的聚集簇。IPA揭示了亚型特异性的通路扰动，包括丢失事件中的生长因子/GPCR信号传导、CN-LOH中的NAD生物合成和昼夜节律调控，以及获得事件中受抑制的干扰素和TLR信号传导，其中TGFB1和TNF成为关键的上游调控因子。
这些发现提示mCAs与加速的表观遗传衰老、免疫细胞组成改变和局部表观遗传重塑相关，其亚型特异性的通路扰动可能反映了允许造血细胞克隆性扩增的不同代偿机制。
查看英文原文 English abstract
Mosaic chromosomal alterations (mCAs), a type of age-related clonal hematopoiesis, arise from postzygotic chromosomal gains, losses, or copy-neutral loss of heterozygosity (CN-LOH) in hematopoietic cells. DNA methylation serves as a molecular measure of biological aging and can be quantified through methylation-based epigenetic clocks. The extent to which mCAs accelerate epigenetic aging or induce local methylation remodeling is poorly understood.
We analyzed 482 cancer-free participants from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial aged 54-77 at sample collection. Selection was based on mCA status (mCA carriers=261), prior genotyping, adequate DNA age and sex. Illumina MethylationEPIC array data raw IDATs were processed using the ChAMP pipeline with BMIQ normalization and ComBat batch correction. Six established methylation clocks (Horvath2013 and 2018, Hannum, PhenoAge, GrimAge, and DunedinPACE) were implemented using the dnaMethyAge R package to compute residual-based age acceleration. Multivariable linear models adjusted for age, sex, ancestry, smoking, and BMI compared mCA carriers to mCA-free individuals, as well as autosomal, mLOY, mLOX, and multi-mCA subtypes. Immune cell composition was estimated with EpiDISH using the IDOL-optimized FlowSorted.BloodExtended.EPIC reference. To identify local methylation effects, ordinary least squares regression tested per-CpG beta-values for differential methylation within mCA-affected regions and functional enrichment was performed using Ingenuity Pathway Analysis (IPA).
Across six epigenetic clocks, mCA carriers showed higher epigenetic age acceleration vs mCA-free (e.g., PhenoAge beta=3.46, 95% CI 1.670-5.22, p=1.32x10 -4 ), with the largest effect sizes observed for autosomal mCAs. Methylation-based deconvolution of whole blood revealed shifts in leukocyte composition, including higher memory B-cell and lower CD4memory-cell proportions in participants with multiple mCAs (B-cell: beta=0.024, p=2.0x10 -8 ; CD4: beta=-0.017, p=0.017). Analyses of methylation levels at each CpG site within mCA regions identified 2,553 significant probes (1,973 hypo- and 580 hyper-methylated) with significant clusters visible across several CN-LOH and Gain regions. IPA revealed subtype-specific pathway perturbations, including growth-factor/GPCR signaling in Loss events , NAD biosynthesis and circadian regulation in CN-LOH, and suppressed interferon and TLR signaling in Gain events, with TGFB1 and TNF emerging as key upstream regulators.
These findings suggest mCAs are associated with accelerated epigenetic aging, altered immune-cell composition, and localized epigenetic remodeling, with subtype-specific pathway disruptions that may reflect distinct compensatory mechanisms permitting clonal expansion in hematopoietic cells.
利益披露 Disclosure
C. D. Young, None.