Fig. 7: Functional validation of MN1 and ATXN1 suggests a role in drug resistance.

a Venn diagrams presenting overlap of 3D gene-based lists with a list of the most significantly differential genes from a meta-analysis of three microarray datasets. b Example shown for PASYFN of an A to B compartment switch shared by 4 patient pairs at the MN1 gene locus including TAD activity, V4C signal, A/B compartments, RNA-seq, and ATAC-seq tracks. c Box plot demonstrating a decrease in MN1 gene expression in tpm (left) and decrease in Cscore (right) in the 4 patient pairs with the A to B compartment switch. Significant differences were calculated using paired t test (*p < 0.05). Boxplots show medians (horizontal line in each box), interquartile ranges (boxes), 1.5 interquartile (whiskers) and each point represents a patient with pairs connected by lines. d Linear regression model demonstrating positive correlation between compartment and gene expression changes at the MN1 locus for patients with differential expression absL2FC > 1.0 (n = 7). e Hi-C contact matrices presenting a TAD increased at relapse in 5 of 12 patient pairs at the ATXN1 locus (Diagnosis, Relapse, and L2FC (Relapse/Diagnosis) from top to bottom). f Box plots demonstrating increased ATXN1 gene expression (top) and increased intra-TAD activity (bottom) in the 5 patient pairs upon relapse. Significant differences were calculated using paired t test (*p < 0.05). Boxplots show medians (horizontal line in each box), interquartile ranges (boxes), 1.5 interquartile (whiskers) and each point represents a patient with pairs connected by lines. g Cell viability (left) and apoptosis assays (right) demonstrating increased sensitivity to treatment with Prednisolone in SEM cells overexpressing MN1 compared to empty vector control (EV). h Cell viability (left) and apoptosis assays (right) demonstrating increased resistance to treatment with Prednisolone in 697 cells overexpressing ATXN1 compared to EV. Cell viability graphs shown (g, h) are one experiment representative of three independent experiments, each with technical triplicates. The dots represent the mean of technical triplicates for that experiment with standard deviation shown. Curve represents the nonlinear fit of transformed X. The null hypothesis of one curve fits all datasets was rejected with p < 0.001 (g, h). Apoptosis graphs shown represents the mean and standard deviation of 4 (g) and 3 (h) individual experiments. Statistical significance shown based on unpaired t test with Welch correction with p value indicated.