Fig 1: Up-regulation of a B-cell developmental gene regulatory network in infant AML.(A-C) Upregulation of LIN28B and its target genes HMGA2 and IGF2BP3 in infant AML. (D, E) BRD4 and MYC, which can form an auto-regulatory loop, are both up-regulated in infant AML, and there is a concomitant positive correlation between LIN28B and MYC expression (F). (G) Genes in a well-studied set of gene regulatory interactions involved in B-cell development are differentially regulated (cyan colored nodes) in AML. Genes marked by * are also known targets of ETS1, which is also highly up-regulated in infant AML.
Fig 2: Micro RNAs in infant AML.(A) Volcano plot showing differentially expressed miRNAs in infants versus children >5 years old. miRNAs to the left of the plot are up-regulated in infant AML. Some notable miRNAs are labeled individually. (B) The Let7 family of miRNAs is down-regulated in infant AML. Among Let7 family members, Let7a-2 exhibits particularly strong patterns of mutual exclusion with its putative target genes IGF2BP1, LIN28B, and HMGA2. Consistent with Let7 repression of IGF2BPs, LIN28B expression is correlated with IGF2BP3 expression.
Fig 3: Five B-cell associated genes up-regulated in infant AML are hypomethylated at the DNA level.(A-E) Shown are differentially methylated region plots for ETS1, BRD4, IGF2BP3, POU2AF1, and LIN28B. The chromosome ideogram at the top shows the genomic location considered (red bar) in hg19 coordinates. The genome browser tracks below each ideogram show the locations of known CpG islands (black bars), and all UCSC transcript isoforms (horizontal lines, with intersecting blue bars marking exons). The super-imposed red box marks the region with differentially methylated probes displayed in detail in the panel below. The vertical axis in the differential methylation panels indicates fractional probe methylation level. CpG probes are organized in their chromosomal order along the horizontal axis. The red and blue plot points mark methylation levels in individual samples (blue = infants, red = >5 year olds). The red and blue lines connect the mean values of CpG methylation levels per patient group. (F) The expression if IGF2BP3, which is only differentially-methylated in a promoter CpG island region (panel E), is highly anti-correlated with the average methylation of all IGF2BP3 CpG probes in this region and distinctive in infant AML (red plot points).
Fig 4: B-cell associated genes in infant AML are expressed at functionally significant levels.(A, B) LIN28B, IGF2BP3, and POU2AF1, are expressed at physiologically meaningful levels in infant AML. Shown are real-time quantitative PCR (RT qPCR) mRNA abundance measurements in 23 infant AML samples (22 for POU2AF1) compared to K562 cells. For comparison, expression in a pool of seven normal bone marrow samples is also shown. (C) The expression of CD19 protein in infant AML blasts is at levels comparable to that of B cells. Shown are flow-cytometry mean fluorescence intensity (MFI) values for AML blasts, T cells and B cells from 19 of 22 infant AML samples successfully tested. Inset shows the high correlation of the PAX5 gene and its putative target CD19.
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