Abstract 3662: FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues

Abstract

Abstract FiTAc-seq is an epigenetic method for profiling of active enhancers and promoters in FFPE clinical samples. The protocol is optimized to generate high-quality H3K27Ac ChIP-seq maps from FFPE macrodissected or cored tissues within 4 days. We previously developed FiT-seq, a modified ChIP-seq protocol for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized to resolve H3K27Ac signal. To overcome this limitation, we have modified the tissue homogenization and sonication steps by replacing the proteinase K digestion applied in FiT-seq with extended heating at 65°C in more stringent detergent conditions and minimizing the sonication step. FiTAc-seq produces high-quality genome wide H3K27Ac profiles, and it is suitable to generate enhancer landscapes and super-enhancer annotation. We demonstrate FiTAc-seq applicability for a wide variety of human tumor types, including bladder cancers, breast cancer brain metastasis, melanomas, pancreatic neuroendocrine tumors and seminomas. The unsupervised hierarchical analyses of both enhancer and super-enhancer only H3K27Ac signal clearly identify clusters according to the different tumor types. Moreover, super-enhancer annotation shows lineage-specific transcription factors for the distinct tumor samples. We demonstrate that FiTAc-seq is a robust method suitable for the epigenetic interrogation of archived FFPE clinical samples. The results generated allow the identification of tissue-specific enhancer and SE landscapes, with potential immediate impact on ongoing basic and translational research. Citation Format: Alba Font-Tello, Nikolas Kesten, Yingtian Xie, Len Taing, Joaquim Bellmunt, Myles Brown, Paloma Cejas, Henry Long. FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3662.