PHF6-altered T-ALL harbored epigenetic repressive switch at bivalent promoters and respond to 5-azacitidine and venetoclax
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Purpose: To assess the impact of PHF6 alterations on clinical outcome and therapeutical actionability in T cells acute lymphoblastic leukemia (T-ALL). Experimental Design: We described PHF6 alterations in an adult cohort of T-ALL from the French trial GRAALL 2003/2005 and retrospectively analyzed clinical outcomes between PHF6-altered (PHF6ALT) and wild-type patients. We also used EPIC and ChIP-seq data of patient samples to analyze the epigenetic landscape of PHF6ALT T- ALLs. We consecutively evaluated 5-azacitidine efficacy, alone or combine with venetoclax, in PHF6ALT T-ALL. Results: We show that PHF6 alterations account for 47% of cases in our cohort and demonstrate that PHF6ALT T-ALL presented significantly better clinical outcomes. Integrative analysis of DNA methylation and histone marks shows that PHF6ALT are characterized by DNA hypermethylation and H3K27me3 loss at promoters physiologically bivalent in thymocytes. Using patient-derived xenografts (PDX), we show that PHF6ALT T-ALL respond to the 5-azacytidine alone. Finally, synergism with the BCL2-inhibitor venetoclax was demonstrated in refractory/relapsing PHF6ALT T- ALL using fresh samples. Importantly, we report three cases of refractory/relapsed (R/R) PHF6ALT patients who were successfully treated with this combination. Conclusions: Overall, our study supports the use of PHF6 alterations as a biomarker of sensitivity to 5-azacytidine and venetoclax combination in R/R T-ALL.
