Figure 4 from ROME, an Ancient Gene with a Novel Function in Vertebrates, Is a Key Modulator of Embryonal Development and Cancer Metastasis

Rome knockdown significantly affects calcium signaling and developmental pathways in zebrafish embryos. A, Uniform Manifold Approximation and Projection (UMAP) of 49 annotated clusters from single cells isolated from control MO–injected zebrafish embryos and rome MO–injected zebrafish embryos at 48 hpf. B, Volcano plot showing differentially expressed genes upon rome knockdown by morpholino across all cell populations (pseudobulk). FC, fold change. C and D, Significantly enriched pathways among upregulated genes (C) and downregulated genes (D) from pseudo-bulk differential expression analysis (top 20 pathways, adjusted P value < 0.05). GO, gene ontology. E–H, Violin plots showing significantly increased icn (E), s100t (F), rspo1 (G), and ctslb (H) expression in zebrafish embryos injected with the rome MO compared with that in embryos injected with the control MO. All comparisons shown have an adjusted P value < 0.05 and an average log2 fold change > 0.66 or < −0.66 (denoted by an asterisk: *). I, Treatment with Wnt pathway inhibitor, ICG-001, rescued developmental defects in zebrafish embryos with rome knockdown at 24 hpf and 48 hpf (DMSO group: n = 43; ICG-001 treatment group: n = 41). Statistical significance was calculated via the Fisher exact test (two-sided).