3108 – MOLECULAR MECHANISMS OF LENALIDOMIDE RESISTANCE IN DEL(5Q) MYELODYSPLASTIC SYNDROMES

Abstract

Interstitial deletion of the long arm of chromosome 5 (del(5q)) is the commonest structural genomic variant in myelodysplastic syndromes (MDS). Lenalidomide (LEN) is the treatment of choice for patients with del(5q) MDS. Half of the responding patients become resistant within two years of which around 20% present TP53 mutations at the time of LEN resistance. To identify novel genetic determinants of LEN resistance, we compared protein coding variants from paired samples from 29 del(5q) patients who responded to LEN and eventually became resistant to treatment. Our analysis identified, in addition to TP53, recurrent RUNX1 alterations in relapsed patients. Exposure of del(5q) cell lines to LEN showed upregulation of RUNX1 protein levels and function in a CRBN and TP53 dependent manner. RUNX1 deletion, shRNA-mediated downregulation or RUNX1 mutant expression rendered sensitive cells unresponsive to LEN. LEN-induced IKZF1 degradation released the transcriptional activity of a RUNX1/GATA2 complex to drive megakaryocytic differentiation of del(5q) cells, which was required for Calpain-dependent del(5q) cell death. We confirmed these findings in human CD34+ cells expressing a shRNA targeting CSNK1A1 expression, which reproduce del(5q) cell LEN sensitivity. RUNX1 and TP53 loss-of-function in del(5q) cells blocked LEN induced megakaryocytic differentiation and subsequent cell death. Transcriptome analysis from paired del(5q) MDS patient samples showed loss of megakaryocytic gene signatures at relapse. Our results suggest that GATA2, RUNX1 and TP53 cooperate to drive megakaryocytic differentiation after LEN-mediated degradation of IKZF1. Mutations blocking LEN-induced megakaryocytic differentiation promote drug resistance and activating GATA2 may re-sensitize therapy-resistant del(5q) cells.