MAGE-TAB Version 1.1 Investigation Title Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish Experimental Design case control design Experimental Design Term Source REF EFO Experimental Design Term Accession Number EFO:0001427 Experimental Factor Name genotype Experimental Factor Type genotype Experimental Factor Term Source REF EFO Experimental Factor Term Accession Number EFO_0000513 Person Last Name Robinson Person First Name Mark Person Mid Initials Person Email mark.robinson@imls.uzh.ch Person Phone Person Fax Person Affiliation University of Zurich Person Address Winterthurerstrasse 190 Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Quality Control Type Quality Control Term Source REF Quality Control Term Accession Number Replicate Type Replicate Term Source REF Replicate Term Accession Number Normalization Type Normalization Term Source REF Normalization Term Accession Number Date of Experiment 2016-06-28 Public Release Date 2018-12-01 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Publication Status Term Accession Number Experiment Description Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare, aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases, yet clear causation remains uncertain. In particular, expression of the notochord-controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation, yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here, we apply a zebrafish model of chordoma onset to identify the notochord-transforming potential of tumor-implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury, including a version with augmented transcriptional activity, is insufficient to initiate notochord hyperplasia in vivo. In contrast, the repeatedly chordoma-implicated receptor tyrosine kinase (RTK) genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells, akin to direct activation of Ras. Analysis of transcriptome and sub-cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together, our results provide first in vivo indication for a lack of tumor-initiating potential of Brachyury expression in the notochord, and suggest activated RTK signaling as potent hyperplasia-initiating event in chordoma. Protocol Name P-MTAB-80210 P-MTAB-80211 P-MTAB-80208 P-MTAB-80209 Protocol Type nucleic acid library construction protocol nucleic acid sequencing protocol sample collection protocol nucleic acid extraction protocol Protocol Term Source REF EFO EFO EFO EFO Protocol Term Accession Number EFO_0004184 EFO_0004170 EFO_0005518 EFO_0002944 Protocol Description RNA-seq libraries were constructed using the Truseq stranded total RNA kit. Sequences were collected on a Illumin HiSeq 2500 machine. 8 dpf wildtype and Tg(twhh:Gal4);Tg(UAS:EGFP-HRASV12) were euthanized with 3% Tricaine methanesulfonate (Sigma). Embryos were decapitated and incubated in Tripsin-EDTA (Sigma) for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol-LS (Ambion). We isolated 30-50 notochords per replicate, with a total of 3 replicates per condition (3x wildtype, 3x HRASV12). Notochord RNA was extracted following the manufacturer’s protocol using Trizol-LS. Protocol Parameters Protocol Hardware Illumina HiSeq 2500 Protocol Software Protocol Contact Term Source Name EFO ArrayExpress Term Source File http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/arrayexpress/ Term Source Version 2.38 SDRF File E-MTAB-7349.sdrf.txt Comment [Submitted Name] Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish Comment [SecondaryAccession] ERP111743 Comment [SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/ERR2862349-ERR2862354 Comment [AEExperimentType] RNA-seq of coding RNA Comment[ArrayExpressAccession] E-MTAB-7349