Histone modification profiling of T-cell prolymphocytic leukemia through chromatin immunoprecipitation and sequencing

T-cell prolymphocytic leukemia (T-PLL) is a rare disease with rapid clinical course. Whole-exome and whole-genome sequencing have identified structural alterations in T-PLL, including inversion, translocation and copy number variation. Epigenetic alterations are the hallmark of many cancers. However, genome-wide epigenomic profiles have not been reported in T-PLL. In this study, we generated genome-wide maps of regulatory regions in both T-PLL patients and healthy individuals using H3K4me3 and H3K27ac ChIP-seq. We revealed a global alteration of both promoter and enhancer landscape in T-PLL, which supported the role of epigenetic regulation in transcriptional dysregulation of oncogenes and genes involved in DNA damage response and T-cell activation. ChIP was performed with peripheral blood mononuclear cells (PBMCs) in T-PLL patients and healthy individuals, using anti-H3K27ac antibody (Abcam, Cat. # ab4729) and in-house generated anti-H3K4me3 antibody, as previously described (PMID: 29268714). The internal H3K4me3 antibody was validated by dot blotting with peptide, ChIP-qPCR with known positive and negative targets, and ChIP-seq (PMID: 29268714). PBMCs from T-PLL samples are over 90% leukemic T cells. For the normal, CD3+ enriched PBMCs were selected. ChIP-seq libraries were prepared from about 5 ng ChIP and input DNA using the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI). ChIP enrichment was validated using real-time PCR. Libraries were sequenced from as 2 x 51 bp or 2 x 101 bp on a Illumina HiSeq4000 platform. ---------------------- Authors state that they "will submit raw fastq files to dbGap".