Fig 1: Differential gene expression analysis identifies FOXB1 as a CIC::NUTM1 fusion specific target.(A) log2 counts per million plots of the indicated genes in 293T cells 48 hours after transfection with empty vector (EV) or the indicated fusion-expressing constructs. Per edgeR quasi-likelihood F-test results, ETV1, ETV4, ETV5, and FOXC2 were significantly activated (log2 fold change > 1.5, q-value < 0.001) in both the HA-CIC::DUX4 and HA-CIC(ex20)::NUTM1(ex6) conditions vs EV. However, FOXD3, FOXB1, and SOX2 were only significantly activated in the HA-CIC(ex20)::NUTM1(ex6) condition vs EV. In the HA-CIC(ex20::NUTM1(ex6) vs EV comparison, FOXG1 met the significance threshold but was slightly under the log2 fold change threshold (value: 1.17), but was included due to its role in brain development. FOXG1 did not meet either significance cutoff in HA-CIC::DUX4 vs EV.(B) Immunoblot of 293T cells approximately 48 hours after transfection with empty vector (EV) or the indicated constructs, representative of the same three independent experiments as in Figure 2A but with a different replicate shown.(C) Immunoblot of 293T cells approximately 48 hours after transfection with empty vector (EV), full length HA-CIC(ex18)::NUTM1(ex3), or truncated versions of HA-CIC(ex18)::NUTM1(ex3) that are comprised only of the HA tag motif and the fractional coding sequence of the indicated partner, split at the breakpoint. Representative of the same three independent experiments as in Figure 2C but with a different replicate shown.(D) Immunoblot of 293T cells approximately 48 hours after transfection with empty vector (EV) or one of three versions of HA-CIC(ex20)::NUTM1(ex6): full length (FL), CIC C1 domain deleted (dC1), or CIC C1 domain and HMG box deleted (dC1 + dHMG). Representative of the same three independent experiments as in Figure 2D but with a different replicate shown.