![Figure 1. Genome-wide analysis and comprehensively characterization of somatic non-coding regulatory mutations in T-ALL. (A) Hotspot analysis identified loci with significant enrichment of recurrent noncoding mutations (single nucleotide variants and/or short insertion/deletions). Statistical significance (−log10 [P value], y-axis) is plotted against the respective chromosomal position of each mutation hotspot (x-axis). Dashed horizontal line, genome-wide significance threshold (P = 5 × 10−8); open circles, mutations significantly associated with expression of adjacent genes (TAL1, LMO1); dots below y = 1, sites with only 1 mutation. (B) Association of LMO1 enhancer mutation (11:8289481G>A) with LMO1 overexpression in the discovery cohort. FPKM, fragments per kilobase of transcript per million mapped reads. (C) Patients with TAL1 enhancer mutations (Mut) had the highest TAL1 expression compared with those with an intrachromosomal rearrangement (STIL-TAL1) or those with a wild-type (WT) genotype. (D) Among a panel of T-ALL cell lines, Jurkat cells were identified as having the LMO1 enhancer mutation and LMO1 overexpression. Gray and blue rectangles, T-ALL cases or cell lines with or without the LMO1 enhancer mutation, respectively. (E) All LMO1 enhancer mutation events were completely conserved across patients and created an MYB binding site. (F) In Jurkat cells, binding of MYB, CREBBP, and RUNX1 was detected by ChIP-seq, with the peak precisely superimposing the LMO1 enhancer mutation (red arrow). RNA polymerase II (RNAPII) binding, DNase I hypersensitivity, and H3K27 acetylation confirmed active transcription at this locus. ChIP-seq peak calling was performed using the MACS2 algorithm (enrichment P < 10−7). (G) Further analysis of the ChIP-seq reads of each allele indicates that transcription factor binding and transcription activation were specific to the mutant allele. ChIP-seq and DNase I hypersensitivity signals (y-axis) were normalized to reads per million reads sequenced in each sample. Statistical significance of the differences was estimated by using 2-sided Mann-Whitney-Wilcoxon test (B-C).](https://ash.silverchair-cdn.com/ash/content_public/journal/blood/129/24/10.1182_blood-2017-03-771162/4/blood771162f1.jpeg?Expires=1722538292&Signature=pqHsumMiGgKEK~8BFVGKbNJqJ8iTY8SyHHmc3S4RkBbteXcyKz1evSqYTLpDRlQR2Eh7NonPELbDVHoCcf-0UpLvdpwTBRP5q6o~lqxebQwtWIdB5SM3tC4xzSMY2RN3e9~-rHQcx7D8uCHUwp6fjcmcWrZSPcgMHWydX4ERda5aQgtBlzERphfuhJfS3Uqls5APLaYVKQFgWEJLJeN2Byy8Z6gtxCUHnfHIwZBWS9bTSGkUBxvSPBRgDOn3ijdKZChXNqlHQoWDnb~9AQfZiM1igUfxnP3mOVG~3V1Yh5v5RHemGYNOU6JCTxObfh71VyxXV5frWGJeANnDbuHoSQ__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA)
Genome-wide analysis and comprehensively characterization of somatic non-coding regulatory mutations in T-ALL. (A) Hotspot analysis identified loci with significant enrichment of recurrent noncoding mutations (single nucleotide variants and/or short insertion/deletions). Statistical significance (−log10 [P value], y-axis) is plotted against the respective chromosomal position of each mutation hotspot (x-axis). Dashed horizontal line, genome-wide significance threshold (P = 5 × 10−8); open circles, mutations significantly associated with expression of adjacent genes (TAL1, LMO1); dots below y = 1, sites with only 1 mutation. (B) Association of LMO1 enhancer mutation (11:8289481G>A) with LMO1 overexpression in the discovery cohort. FPKM, fragments per kilobase of transcript per million mapped reads. (C) Patients with TAL1 enhancer mutations (Mut) had the highest TAL1 expression compared with those with an intrachromosomal rearrangement (STIL-TAL1) or those with a wild-type (WT) genotype. (D) Among a panel of T-ALL cell lines, Jurkat cells were identified as having the LMO1 enhancer mutation and LMO1 overexpression. Gray and blue rectangles, T-ALL cases or cell lines with or without the LMO1 enhancer mutation, respectively. (E) All LMO1 enhancer mutation events were completely conserved across patients and created an MYB binding site. (F) In Jurkat cells, binding of MYB, CREBBP, and RUNX1 was detected by ChIP-seq, with the peak precisely superimposing the LMO1 enhancer mutation (red arrow). RNA polymerase II (RNAPII) binding, DNase I hypersensitivity, and H3K27 acetylation confirmed active transcription at this locus. ChIP-seq peak calling was performed using the MACS2 algorithm (enrichment P < 10−7). (G) Further analysis of the ChIP-seq reads of each allele indicates that transcription factor binding and transcription activation were specific to the mutant allele. ChIP-seq and DNase I hypersensitivity signals (y-axis) were normalized to reads per million reads sequenced in each sample. Statistical significance of the differences was estimated by using 2-sided Mann-Whitney-Wilcoxon test (B-C).
