RNA-seq from primary skin fibroblasts, derived of matched pairs of middle and late donor age

Aging signatures developed from a longitudinal study design are dominated by reduced transcription of genes involved in protein synthesis Aging is a multifactorial process where the impact of singular components still remains unclear. Furthermore, previous studies were focused on measuring specific traits such as DNA -methylation and used categorical group-wise designs, unable to capture intra-individual signature changes. Here we have developed a new method for a longitudinal, age-related analysis combining the merits of a pair-wise design with the statistical power of gene set enrichment analysis. We present an integrated analysis, including transcriptional changes and genome-wide epigenetic changes in DNA- methylation, H3K4- and H3K27- histone methylation in promoter regions. We tested our method on a rare collection of paired skin fibroblast samples from male middle age to old age transitions and obtained functional, age-related clusters. By using a set of only ten individuals, we could demonstrate a high overlap of functional terms to previously established tissue-independent age signatures including extracellular matrix, apoptosis and oxidative stress. Importantly, we identify protein translation-related processes as the main cluster of age-driven, specific down regulation. Evaluation of transcriptional changes in matched sample pairs of primary skin fibroblasts from middle and old age.

基于纵向研究设计构建的衰老特征，主要表现为参与蛋白质合成的基因转录水平显著下调。衰老是一个多因素调控的复杂过程，单一组分的具体影响仍未明确。此外，既往研究多聚焦于测量DNA甲基化等特定表观遗传性状，且采用分类分组式研究设计，无法捕捉个体内部的衰老特征动态变化。在此，我们开发了一种新型纵向年龄相关分析方法，融合了配对设计的优势与基因集富集分析（gene set enrichment analysis）的统计效能。本研究开展了整合分析，涵盖转录组变化以及全基因组范围的DNA甲基化、启动子区域H3K4与H3K27组蛋白甲基化等表观遗传组变化。我们通过一组罕见的男性中年至老年过渡阶段的配对皮肤成纤维细胞样本对该方法进行了验证，最终获得了具有功能意义的年龄相关聚类模块。仅通过10名受试者的样本，我们便证实本方法得到的功能术语与既往报道的组织非依赖性衰老特征存在高度重合，这些特征涵盖细胞外基质、细胞凋亡与氧化应激等通路。尤为重要的是，我们发现蛋白质翻译相关通路是年龄驱动的特异性下调的主要聚类模块。本研究针对中年至老年阶段的原代皮肤成纤维细胞配对样本的转录组变化开展了评估。