PO.MCB06.02 · 分子与细胞生物学
DKC1、TERC和TINF2致病性种系变异导致的独特全基因组DNA甲基化特征
Distinct genome wide DNA methylation signatures due to pathogenic germline variants in DKC1 , TERC , and TINF2
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
DKC1、TERC或TINF2中的种系致病性变异（GPVs）会导致端粒维持缺陷，并引起易患癌症的端粒生物学疾病（TBDs）。DNA甲基化（DNAm）可影响TBDs的疾病表现度和外显率；然而，TBDs患者间的表观遗传特征仍未明确。由于端粒缩短是衰老的标志之一，TBDs也为研究其与表观遗传衰老的联系提供了框架。我们旨在识别DNAm改变并评估TBDs患者的表观遗传衰老。使用Illumina Infinium Methylation EPICv2芯片，对参与我们经IRB批准研究（NCT00027274）的、携带杂合TERC（n=15）或TINF2（n=13）GPVs的个体、半合子DKC1男性（n=7）以及41名对照的血液样本进行全基因组DNAm分析。差异甲基化探针（DMP）分析使用limma进行，校正了年龄、性别、DNAm推导的细胞类型组成和家系结构（FDR < 0.05且|Δbeta| ≥ 0.20）；组间差异采用混合效应回归模型进行评估。差异甲基化区域（DMRs）使用DMRcate识别（HMFDR < 0.05；|平均Δbeta| ≥ 0.10）。DMP相关基因的功能富集通过使用missMethyl的KEGG通路分析进行评估。表观遗传衰老使用DunedinPACE算法进行估计。我们分别在TINF2、DKC1和TERC中识别出499、167和164个DMPs。高甲基化主要见于OpenSea区域（59–79%），但TERC除外，其在CpG岛中呈现富集（45%）。在所有队列中，低甲基化探针主要位于OpenSea（≥90%）。基因组定位显示TERC携带者中X染色体上高甲基化富集，而TINF2和DKC1则表现出广泛的常染色体改变。我们在TINF2中检测到403个DMRs，DKC1中158个，TERC中119个，主要位于启动子近端（21–30%）和内含子（27–38%）区段内。启动子高甲基化在TERC和DKC1中最常见，而TINF2表现出内含子高甲基化（36%）。有9个具有启动子高甲基化和5个具有低甲基化的基因在所有患者中反复被检测到。通路分析显示在造血谱系和钙信号通路中富集，并在免疫（DKC1）、干细胞（TERC）和生长因子（TINF2）通路中呈现基因特异性趋势。所有患者的表观遗传衰老均加速，在DKC1（beta=0.225，p<0.001）和TINF2（beta=0.190，p<0.001）中最为显著。我们在TBDs个体中检测到独特而又趋同的DNAm特征。携带TINF2 GPVs的个体表现出最广泛的甲基化重塑。所有患者均表现出加速的表观遗传衰老。这些发现提示DNAm改变伴随TBDs中的端粒功能障碍，并强调需要整合多组学和纵向研究，以阐明其机制基础、组织特异性和临床意义。
查看英文原文 English abstract
Germline pathogenic variants (GPVs) in DKC1 , TERC , or TINF2 lead to defective telomere maintenance and cause the cancer-prone telomere biology disorders (TBDs). DNA methylation (DNAm) can contribute to disease expressivity and penetrance in TBDs; however, epigenetic signatures across patients with TBDs remain undefined. As telomere shortening is a hallmark of aging, TBDs also offer a framework to study its link to epigenetic aging. We sought to identify DNAm alterations and evaluate epigenetic aging in patients with TBDs. Genome-wide DNAm profiling was performed using the Illumina Infinium Methylation EPICv2 array on blood samples from individuals with heterozygous TERC (n=15) or TINF2 (n=13) GPVs, hemizygous DKC1 males (n=7), and 41 controls participating in our IRB-approved study (NCT00027274). Differentially methylated probe (DMP) analysis was conducted using limma , adjusting for age, sex, DNAm-derived cell type composition, and family structure (FDR < 0.05 and |Δbeta| ≥ 0.20); group differences were evaluated with mixed-effects regression models. Differentially methylated regions (DMRs) were identified with DMRcate (HMFDR < 0.05; |mean Δbeta| ≥ 0.10). Functional enrichment of DMP-associated genes was assessed via KEGG pathway analysis using missMethyl . Epigenetic aging was estimated using the DunedinPACE algorithm. We identified 499, 167, and 164 DMPs in TINF2 , DKC1 , and TERC , respectively. Hypermethylation was mainly found in OpenSea regions (59-79%), except for TERC , which showed enrichment in CpG islands (45%). Hypomethylated probes were largely OpenSea (≥90%) across all cohorts. Genomic mapping showed enrichment of hypermethylation on chromosome X in TERC carriers, whereas TINF2 and DKC1 showed widespread autosomal changes. We detected 403 DMRs in TINF2 , 158 in DKC1 , and 119 in TERC , predominantly within promoter-proximal (21-30%) and intronic (27-38%) segments. Promoter hypermethylation was most common in TERC and DKC1 , whereas TINF2 exhibited intronic hypermethylation (36%). Nine genes with promoter hypermethylation and five with hypomethylation were recurrently detected across all patients. Pathway analysis showed enrichment in hematopoietic lineage and calcium signaling, with gene-specific trends in immune ( DKC1 ), stem cell ( TERC ), and growth factor ( TINF2 ) pathways. Epigenetic aging was accelerated in all patients, most prominently in DKC1 (beta=0.225, p<0.001) and TINF2 (beta=0.190, p<0.001). We detected distinct yet convergent DNAm signatures across individuals with TBDs. Individuals with GPVs in TINF2 exhibited the most extensive methylation remodeling. All patients demonstrated accelerated epigenetic aging. These findings suggest that DNAm alterations accompany telomere dysfunction in TBDs and underscore the need for integrated multi-omic and longitudinal studies to clarify its mechanistic basis, tissue specificity, and clinical implications.
利益披露 Disclosure
K. De Andrade, None..
G. Ney, None..
T. Zhao, None..
S. Gaddam, None..
J. Liu, None..
K. Jones, None..
L. J. McReynolds, None..
N. Giri, None..
S. A. Savage, None.