The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10–20 tissue sections or whole tissue blocks, which prevents better resolved analyses. But it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissues of interest are limited. Here, we present FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq), the first highly sensitive method to efficiently profile histone modifications in FFPE tissues by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7−pA−Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We proved a very small piece of FFPE tissue section containing ∼4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. H3K27ac FACT-seq revealed disease-specific super enhancers in the archived FFPE human colorectal and human glioblastoma cancer tissue. In summary, FACT-seq allows decoding the histone modifications in archival FFPE tissues with high sensitivity and help researchers to better understand epigenetic regulation in cancer and human disease.

中文翻译：

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FACT-seq：分析福尔马林固定石蜡包埋样品中的组蛋白修饰，细胞数较少

基础研究和转化癌症研究中的大多数活检都以存档的福尔马林固定石蜡包埋 (FFPE) 样本的形式保存。分析存档 FFPE 组织中的组蛋白修饰对于了解人类疾病中的基因调控至关重要。当前来自 FFPE 样本的全基因组组蛋白修饰分析研究所需的输入是 10-20 个组织切片或整个组织块，这阻碍了更好的解析分析。但由于感兴趣的临床组织有限，因此需要在分析中消耗最少量的 FFPE 组织切片。在这里，我们展示了带有抗体引导的染色质标记和测序 (FACT-seq) 的 FFPE 组织，第一种通过结合高活性 Tn5 转座酶和蛋白 A (T7-pA-Tn5) 转座和 T7 体外转录的新型融合蛋白来有效分析 FFPE 组织中组蛋白修饰的高灵敏度方法。FACT-seq 从具有少量 FFPE 核的不同组蛋白修饰生成高质量的染色质图谱。我们证明了一小块含有约 4000 个细胞核的 FFPE 组织切片足以用 FACT-seq 解码 H3K27ac 修饰。H3K27ac FACT-seq 在存档的 FFPE 人结肠直肠癌和人胶质母细胞瘤癌组织中揭示了疾病特异性超级增强剂。总之，FACT-seq 允许以高灵敏度解码存档 FFPE 组织中的组蛋白修饰，并帮助研究人员更好地了解癌症和人类疾病中的表观遗传调控。