基于转录组和DNA甲基化的细胞类型解卷产生了差异性基因表达和差异性甲基化的类似估计
Emily R Hannon1,2, Carmen J Marsit3, Arlene E Dent4,5
1Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA. erh90@case.edu.
BioData mining
|July 11, 2024
概括
血液样本中的细胞类型比例以类似的方式被转录组和甲基组解卷方法捕获. 这种一致性对于准确的基因表达和DNA甲基化研究至关重要.
科学领域:
- 基因组学就是基因组学.
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
- 免疫学 免疫学 免疫学
背景情况:
- 周围血液单核细胞 (PBMC) 中的细胞类型组成可以显著影响基因表达和DNA甲基化分析.
- 准确的细胞类型解对于可靠的差异基因表达 (DEG) 和差异DNA甲基化 (DMP) 研究至关重要.
- 之前的研究还没有完全比较使用转录组和甲基组数据的解卷方法.
研究的目的:
- 调查从转录组与甲基组数据中得出的细胞类型比例如何影响DEG和DMP估计.
- 为了比较两种解卷方法 (Cibersortx和IDOL) 的有效性,从RNA和DNA分析PBMC细胞类型比例.
主要方法:
- 转录基因组和DNA甲基化 (DNAm) 数据从肯尼亚儿童的PBMCs (n=8) 收集,这些数据是在不复杂的疟疾周围的多个时间点.
- 用Cibersortx进行了细胞类型解卷,用于转录组数据和IDOL用于DNAm数据.
- 用细胞类型调整的建模来检测时间点之间的DEG和DMP.
主要成果:
- 在大多数主要细胞类型中,通过两种解方法估计的细胞类型比例之间观察到高相关性 (r=0.60-0.96).
- 对细胞类型比例,DEG和DMP的估计在两种方法中基本一致.
- 方法之间的最大差异是在估计中性粒细胞比例时发现的.
结论:
- 转录组和甲基组解卷方法在大多数主要细胞类型中以类似的方式捕捉细胞类型比例的变化.
- 这些发现表明,这两种方法对于大多数细胞类型都是可靠的,这有助于在PBMC中进行可靠的下游分析.
- 在比较转录组和甲基组解卷的结果时,可能需要仔细考虑中性粒细胞估计.
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