Ben Fisher

Chordoma is a rare and aggressive sarcoma that develops along the craniospinal axis, most commonly within the sacral and clival regions. Treatment options are limited due to chordoma's ability to invade neural and vascular structures and resistance to chemotherapy. Chordomas are hypothesized to arise from notochordal remnants and our data has identified chordoma subgroups through DNA methylation and bulk RNA sequencing. Little is known about the developmental origin of chordomas. This study analyzed notochord-like cells (NCLs) and neuromesodermal progenitors (NMPs) as potential cells of origin for chordoma subgroups. Induced pluripotent stem cells (iPSC) were differentiated into NCLs and NMPs over the course of 7 and 5 days, respectively. NCL differentiation was confirmed through qRT-PCR by measuring expression levels of transcription factors necessary for development including Noto, FoxA2, and TBXT while NMP was confirmed through expression of transcription factors Sox2 and TBXT. In line with previous literature and preliminary data, NCLs significantly increase expression of all three transcription factors between days 4-7 and NMPs increase expression of TBXT between days 3-5 and show an initial high expression in Sox2 followed by a significant decrease between days 3-4. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) was utilized to establish the chromatin landscape of active, enhancer, and repressive histone marks. A library was prepared from the extracted DNA and is currently being sequenced. The resulting data will be compared with chordoma subgrouping data to determine potential cell(s) of origin and to better understand the permissive chromatin landscape for chordoma tumorigenesis.