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ccr-23-2159_supplementary_table_s2_suppts2.xlsx (18.37 kB)

Supplementary Table S2 from PHF6-altered T-ALL Harbor Epigenetic Repressive Switch at Bivalent Promoters and Respond to 5-Azacitidine and Venetoclax

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posted on 2024-01-05, 08:40 authored by Antoine Pinton, Lucien Courtois, Charlotte Doublet, Aurélie Cabannes-Hamy, Guillaume Andrieu, Charlotte Smith, Estelle Balducci, Agata Cieslak, Aurore Touzart, Mathieu Simonin, Véronique Lhéritier, Françoise Huguet, Marie Balsat, Hervé Dombret, Philippe Rousselot, Salvatore Spicuglia, Elizabeth Macintyre, Nicolas Boissel, Vahid Asnafi

Bivalent genes hypermethylated in PHF6 altered T-ALL and targeted by PHF6

Funding

Assistance Publique - Hôpitaux de Paris (AP-HP)

Schweizerische Arbeitsgemeinschaft für Klinische Krebsforschung (SAKK)

Fondation ARC pour la Recherche sur le Cancer (ARC)

History

ARTICLE ABSTRACT

To assess the impact of PHF6 alterations on clinical outcome and therapeutical actionability in T-cell acute lymphoblastic leukemia (T-ALL). We described PHF6 alterations in an adult cohort of T-ALL from the French trial Group for Research on Adult Acute Lymphoblastic Leukemia (GRAALL)-2003/2005 and retrospectively analyzed clinical outcomes between PHF6-altered (PHF6ALT) and wild-type patients. We also used EPIC and chromatin immunoprecipitation sequencing data of patient samples to analyze the epigenetic landscape of PHF6ALT T-ALLs. We consecutively evaluated 5-azacitidine efficacy, alone or combined with venetoclax, in PHF6ALT T-ALL. 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, we show that PHF6ALT T-ALL respond to the 5-azacytidine alone. Finally, synergism with the BCL2-inhibitor venetoclax was demonstrated in refractory/relapsing (R/R) PHF6ALT T-ALL using fresh samples. Importantly, we report three cases of R/R PHF6ALT patients who were successfully treated with this combination. 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.