The 3D chromatin landscape of rhabdomyosarcoma

Abstract

Rhabdomyosarcoma (RMS) is a pediatric soft tissue cancer with a lack of precision therapy option for 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 most common 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. Our comprehensive analysis provides high-depth chromatin interactivity maps for contextualizing gene regulation events identification of functionally critical chromatin domains in RMS.

Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo

“…In cell culture, PAX3::FOXO1 can localize to heterochromatin fractions, asymmetrically flank the repressive H3K9me3 histone mark, and bind within generally repressive B-chromatin compartments, in addition to binding at active enhancers and within more transcriptionally active A-compartments 17,20,63 . We observed a similar pattern in our zebrafish model, with PAX3::FOXO1 invading regions originally and persistently devoid of chromatin accessibility (Fig.…”

Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing

“…Of note, we report a specific application of our PerCell method to precisely map the genome-wide binding of a transcription factor (TF) chimera occurring in a rare childhood sarcoma (see Procedure, and Figure 4), for which we have developed new, rapid, and in vivo expression systems in zebrafish rhabdomyosarcoma models (Figure 4a,b), based on earlier contributions in this area 16 . Notably, when we rapidly express the TF-chimera PAX3::FOXO1 in vivo, PerCell normalization of anti-FOXO1 ChIP-seq 17,18 reveals quantitative changes in the induction of H3K27ac at key target genes and binding sites (Figure 4,c,d). This is especially notable given that (1) these binding sites normally lack H3K27ac and (2) enhancer activation is typically driven by pluripotency transcription factors during these early embryonic zebrafish timepoints 19,20 .…”