Integrated epigenomic analysis identifies structural alterations associated with oncogenic gene expression in liposarcoma

Liposarcoma (LPS) is the most common soft-tissue sarcoma in adults. The two most frequent subtypes well differentiated (WD) and dedifferentiated (DD) LPS are often marked with the giant chromosome and the amplifications of chromosome 12q13-15. However, it remains unknown how this genomic aberrancy contributes to the dysregulation of the oncogenes. Here, we reported a comprehensive molecular characterization of both tumor and normal tissues from the same batch of LPS patients, including Hi-C, H3K27ac ChIP-seq, RNA-seq and WGS datasets. We identified a library of tumor-specific enhancers that may play a critical role in oncogenesis. We also demonstrated the enhancer co-amplification and hijacking events involved with proto-oncogenes such as MDM2, CDK4 and HMGA2, which have not been previously reported and as a novel mechanism to upregulate these genes. By combining Hi-C, optical mapping, Nanopore long reads and WGS data, we partially resolved complex structure variations (SVs) and reconstructed the local genome and the giant chromosome. We further validated the presence of multiple copies of MDM2 and CDK4 are located on the giant chromosome by fluorescent in situ hybridization (FISH). Consequently, this study provides a comprehensive resource for further research in LPS. We started with 5 pairs of WD-LPS, 14 pairs of DD-LPS patient samples, and 1 DD-LPS cell line. Each pair of patient samples contains one tumor tissue and one matched peritumoral tissue as control. To profile the transcribed regions and to reveal the differential transcriptomes between tumors and peritumoral tissues, we performed mRNA sequencing (mRNA-seq) in all patient samples and cell lines. In 4 pairs of DD-LPS patient samples (P241, P298, P69 and P209) and 1 DD-LPS cell line (Lipo863B), we performed 1) chromatin immunoprecipitation followed by DNA-seq (ChIP-seq) for histone modifications H3 lysine 27 acetylation (H3K27ac), to chart the open chromatin regions and DD-LPS-specific regulatory elements, such as enhancers; 2) Hi-C experiments to study high-order chromatin structure and link distal enhancers to their target genes; 3) whole genome sequencing (WGS) to profile CNVs and dissect genome rearrangements. To better reveal the sequence details of genome rearrangements, we performed Nanopore long-read sequencing and BioNano optical mapping in Lipo863B cells to help assemble the rearranged regions. In total, we generated 71 genomic datasets, including 62 for the patient tissue samples and 9 for the cell line Lipo863B. Raw data not provided for patient samples due to patient privacy concerns.