IRX3 is aberrantly expressed in T-ALL and resides in a shared topologically associated domain with E-P contacts to neighboring genes FTO, CRNDE, and IRX5. (A) Schematic outlining the comparative analysis conducted on bulk RNA-seq from developing T-cell subsets (National Center for Biotechnology Information Gene Expression Omnibus accession #GSE69239) and bulk RNA-seq from St. Jude’s pediatric T-ALL cohort (Liu et al, n = 264)²⁰ to identify aberrantly expressed genes. (B) Box and whisker plot showing expression of top 50 genes aberrantly expressed in the St. Jude’s pediatric T-ALL cohort (n = 264) compared with normal hematopoietic progenitors (NCBI GEO accession #GSE69239); hematopoietic stem cells (HSCs), lymphoid primed multipotent progenitors (LMPPs), common lymphoid progenitors (CLPs), and T-cell subsets (Thy1-6). Expression values for T-cell subsets are from 2 replicates for each population and expression is FPKM averaged for each cell type. T-ALL cohort genes are ranked along the x-axis by mean expression. (C) Line graph tracking IRX3, LMO2, and TAL1 expression by RNA-seq across hematopoietic and thymic progenitors. RNA-seq from NCBI GEO accession #GSE69239, with the following immunophenotypic definitions: from bone marrow CD34⁺ cells, CD34⁺CD38^–Lin⁻ (HSCs), CD34⁺CD45RA⁺CD38⁺CD10⁻CD62L^hiLin⁻ (LMPPs), CD34⁺CD38⁺CD10⁺CD45RA⁺Lin⁻ (CLPs); from thymic CD34⁺ cells, CD34⁺CD7⁻CD1a⁻CD4⁻CD8⁻ (Thy1), CD34⁺CD7⁺CD1a⁻CD4⁻CD8⁻ (Thy2), and CD34⁺CD7⁺CD1a⁺CD4⁻CD8⁻ (Thy3); from thymic CD34⁻ cells, CD4⁺CD8⁺ (Thy4), CD3⁺CD4⁺CD8⁻ (Thy5), and CD3⁺CD4⁻CD8⁺ (Thy6). (D) Violin plot showing IRX3 expression (FPKM) by RNA-seq from the St. Jude primary T-ALL cohort separated by class-defining oncogenic subtypes (n = 264). (E) Bar chart showing IRX3 expression (FPKM) by RNA-seq from T-ALL cell lines (n = 24) and labeled by oncogenic subtype. (F) E-P interactions about the IRX3 locus mapped by HiChIP after pull-down for H3K27ac from the IRX3-positive CUTTL1 T-ALL cell line (NCBI GEO accession #GSE115896) and ChIP-seq for H3K27ac in CUTTL1 cells. Loops between IRX3 and cCREs for IRX3 are highlighted in red and indicated with arrows. (G) Ranked gene list by comparing IRX3-positive (top, n = 59) vs IRX3-negative (bottom, n = 59) T-ALL samples by RNA-seq from the St. Jude cohort. The y-axis ranking score metric for each gene was calculated by the GSEA “Signal2Noise” computational method for categorical phenotypes. Genes are listed along the x-axis in order of the ranked score. cCREs, candidate cis-regulatory elements.