Langevin Scott M, Houseman E Andres, Accomando William P, Koestler Devin C, Christensen Brock C, Nelson Heather H, Karagas Margaret R, Marsit Carmen J, Wiencke John K, Kelsey Karl T
Department of Environmental Health; University of Cincinnati College of Medicine; Cincinnati, OH USA; Department of Epidemiology; Brown University; Providence, RI USA.
Department of Biostatistics; Oregon State University College of Public Health and Human Sciences; Corvallis, OR USA.
Epigenetics. 2014 Jun;9(6):884-95. doi: 10.4161/epi.28575. Epub 2014 Mar 26.
Epigenome-wide studies of DNA methylation using blood-derived DNA from cancer patients are complicated by the heterogeneity of cell types within blood and the associated cell lineage specification of DNA methylation signatures. Here, we applied a novel set of analytic approaches to assess the association between cancer case-status and DNA methylation adjusted for leukocyte variation using blood specimens from three case-control cancer studies (bladder: 223 cases, 205 controls; head and neck: 92 cases, 92 controls; and ovarian: 131 cases, 274 controls). Using previously published data on leukocyte-specific CpG loci and a recently described approach to deconvolute subject-specific blood composition, we performed an epigenome-wide analysis to examine the association between blood-based DNA methylation patterns and each of the three aforementioned solid tumor types adjusted for cellular heterogeneity in blood. After adjusting for leukocyte profile in our epigenome-wide analysis, the omnibus association between case-status and methylation was significant for all three studies (bladder cancer: P = 0.047; HNSCC: P = 0.013; ovarian cancer: P = 0.0002). Subsequent analyses revealed that CpG sites associated with cancer were enriched for transcription factor binding motifs involved with cancer-associated pathways. These results support the existence of cancer-associated DNA methylation profiles in the blood of solid tumor patients that are independent of alterations in normal leukocyte distributions. Adoption of the methods developed here will make it feasible to rigorously assess the influence of variability of normal leukocyte profiles when investigating cancer related changes in blood-based epigenome-wide association studies.
利用癌症患者血液来源的DNA进行全表观基因组DNA甲基化研究，因血液中细胞类型的异质性以及DNA甲基化特征相关的细胞谱系特异性而变得复杂。在此，我们应用了一套新颖的分析方法，使用来自三项病例对照癌症研究（膀胱癌：223例病例，205例对照；头颈癌：92例病例，92例对照；卵巢癌：131例病例，274例对照）的血液样本，评估癌症病例状态与针对白细胞变异进行调整后的DNA甲基化之间的关联。利用先前发表的关于白细胞特异性CpG位点的数据以及最近描述的一种反卷积个体特异性血液组成的方法，我们进行了全表观基因组分析，以研究血液中基于DNA的甲基化模式与上述三种实体瘤类型中每一种之间的关联，并针对血液中的细胞异质性进行了调整。在我们的全表观基因组分析中对白细胞谱进行调整后，所有三项研究中病例状态与甲基化之间的总体关联均具有统计学意义（膀胱癌：P = 0.047；头颈鳞状细胞癌：P = 0.013；卵巢癌：P = 0.0002）。随后的分析表明，与癌症相关的CpG位点富含与癌症相关途径有关的转录因子结合基序。这些结果支持实体瘤患者血液中存在与癌症相关的DNA甲基化谱，且这些谱与正常白细胞分布的改变无关。采用此处开发的方法将使得在基于血液的全表观基因组关联研究中调查癌症相关变化时，能够严格评估正常白细胞谱变异性的影响。
