Pax3 loss of function delays tumor progression in kRAS-induced zebrafish rhabdomyosarcoma models

Rhabdomyosarcoma is a soft tissue cancer that arises in skeletal muscle due to mutations in myogenic progenitors that lead to ineffective differentiation and malignant transformation. The transcription factors Pax3 and Pax7 and their down-stream target genes are tightly linked with the fusion positive alveolar subtype, whereas the RAS pathway is usually involved in the embryonic, non-fusion variant. Here, we analyse the role of Pax3 in a non-fusion context, by linking alterations in gene expression in pax3a/pax3b double mutant zebrafish with tumour progression in kRAS-induced rhabdomyosarcoma tumours. Several genes in the RAS signalling pathway, including MAPK signalling pathway, were significantly down-regulated in pax3a/pax3b double mutant zebrafish. Onset and progression of rhabdomyosarcoma tumours were also delayed in the pax3a/pax3b double mutant zebrafish indicating that Pax3 transcription factors have an unappreciated role in mediating malignancy also in non-fusion rhabdomyosarcoma. Zebrafish embryos from wild type and pax3a-/-(umu5); pax3b-/-(umu6) homozygous double mutants were collected at 42 hpf for RNA preparation. A total of six samples, two triplicates each, were included in RNA sequencing. poly-A selection libraries were prepared, pooled and sequenced on a 1/4th NovaSeq600 S4 lane, with 2x150bp reads