Harnessing the MYB-dependent TAL1 5'super-enhancer for targeted therapy in T-ALL

Abstract

The acquisition of genetic abnormalities engendering oncogene dysregulation underpins cancer development. Certain proto-oncogenes possess several dysregulation mechanisms, yet how each mechanism impacts clinical outcome is unclear. Using T-cell acute lymphoblastic leukemia (T-ALL) as an example, we show that patients harboring 5'super-enhancer (5'SE) mutations of the TAL1 oncogene identifies a specific patient subgroup with poor prognosis irrespective of the level of oncogene dysregulation. Remarkably, the MYB dependent oncogenic 5'SE can be targeted using Mebendazole to induce MYB protein degradation and T-ALL cell death. Of note Mebendazole treatment demonstrated efficacy in vivo in T-ALL preclinical models. Our work provides proof of concept that within a specific oncogene driven cancer, the mechanism of oncogene dysregulation rather than the oncogene itself can identify clinically distinct patient subgroups and pave the way for future super-enhancer targeting therapy.

Keywords: Cancer; Oncogene; Super-enhancer; Targeted therapy.

Fig. 1

Mebendazole demonstrates anti-leukemic activity in 5’SE T-ALLs with poor clinical outcome due to MYB-mediated TAL1 inhibition. A 5’microinsertion sequences aligned to the normal physiological sequence (Hg38). The red arrow denotes the mutation insertion site. All TAL1 super-enhancer mutations introduce de novo MYB binding sites (underlined). B The relative TAL1 expression normalized to ABL + GAPDH expression in the thymus and T-ALL patients. Kruskal–Wallis; 5’SE vs. SIL-TAL1 p-adj = 0.5, 5’SE vs. TAL1-TCRD p-adj = 0.99, SIL-TAL1 vs. TAL1-TCRD p-adj = 0.97. C TAL1 protein expression in 5’SE compared with SIL-TAL1 T-ALL. Left Panel T-ALL cell lines, Right Panel PDX. Histone was used as a loading control. D Cumulative Incidence of relapse (CIR) of 5’SE, SIL-TAL1 and Other T-ALL. E Kaplan Meier depicting overall (OS) survival of 5’SE, SIL-TAL1 and other T-ALL. F Viability curves of 5’SE, SIL-TAL1, and Other T-ALL (Cell lines + PDX) at increasing Mebendazole concentrations. Viability was normalized to DMSO controls. The Mean and SEM are shown of duplicate samples. (Two-way ANOVA; 5’SE vs. SIL-TAL1 and Other T-ALL p < 0.0001). G MYB and TAL1 protein expression after 48 h Mebendazole exposure in the Jurkat cell line, a representative 5’SE, SIL-TAL1 and TAL1 negative (TAL1-) PDX with corresponding TAL1 mRNA expression for TAL1 + T-ALL (Right Panel). TAL1 expression was normalized to GAPDH

Fig. 2

Mebendazole delays tumor progression in 5’SE T-ALLs in vivo. A Schematic showing Mebendazole treatment settings. Adapted from “Mouse Experimental Timeline”, by BioRender.com (2022). Retrieved from https://app.biorender.com/biorender-templates. B Bioluminescence imaging of NSG recipient mice 31 days after injection with Jurkat cells. Representative images are shown. Mann–Whitney; Control vs. Preventive p = 0.03, Control vs. Curative p = 0.01. The Mean and SEM are shown. C hCD45 staining of bone marrow cells 28 days after injection with Jurkat luciferase expressing cells. Mann–Whitney; Control vs. Preventive p = 0.01, Control vs. Curative p = 0.02. The mean and SEM are shown. D Flow Cytometric peripheral blood staining of hCD45 21 days after injection with 5’SE PDX cells. Control vs. Preventive p = 0.03, Control vs. Curative p = 0.02. The mean and SEM are shown. E Kaplan Meier survival curves for Control, Preventive and Curative mice. Log-rank (Mantel-Cox) Test; Control vs. Preventive vs. Curative p = 0.007, Control vs. Preventive p = 0.005, Control vs. Curative p = 0.001. F Kaplan Meier survival curves for Control, Preventive and Curative 5’SE PDX mice. Log-rank (Mantel-Cox) Test; Control vs. Preventive vs. Curative p = 0.004, Control vs. Preventive p = 0.009, Control vs. Curative p = 0.01