The 3D chromatin landscape of rhabdomyosarcoma [HiC]

Rhabdomyosarcoma (RMS) is a pediatric soft tissue cancer with no precision therapy available for affected patients. We hypothesized that with a general paucity of known mutations in RMS, chromatin structural driving mechanisms are essential for tumor proliferation. Thus, we carried out high-depth in situ Hi-C in representative cell lines and patient-derived xenografts to understand chromatin architecture in each major RMS subtype. We report a comprehensive 3D chromatin structural analysis and characterization of fusion-positive (FP-RMS) and fusion-negative rhabdomyosarcoma (FN-RMS). We have generated spike-in in situ Hi-C chromatin interaction maps for the commonest FP-RMS and FN-RMS cell lines, and compared our data with patient derived xenograft (PDX) models. In our studies we uncover common and distinct structural elements in large Mb-scale chromatin compartments, tumor-essential genes within variable topologically associating domains, and unique patterns of structural variation. This study enables a comprehensive resource for contextualizing gene regulation events in RMS, and high-depth chromatin interactivity maps for identification of functionally critical chromatin domains in this tumor. Overall design: Human rhabdomyosarcoma (RMS) cell lines RD, SMS-CTR, Rh30 and Rh41 cells were spiked in with 20% mouse myoblasts (C2C12) and fixed with Formaldehyde. Mouse chromatin reads were used as reference to normalize the RMS samples. Two independent biological replicates for each cell line were combined informatically to get contact maps with 30 million valid, long-range cis contacts.