Systematic chemical and molecular profiling of MLL-rearranged infant acute lymphoblastic leukemia reveals efficacy of romidepsin

Abstract

To address the poor prognosis of mixed lineage leukemia (MLL)-rearranged infant acute lymphoblastic leukemia (iALL), we generated a panel of cell lines from primary patient samples and investigated cytotoxic responses to contemporary and novel Food and Drug Administration-approved chemotherapeutics. To characterize representation of primary disease within cell lines, molecular features were compared using RNA-sequencing and cytogenetics. High-throughput screening revealed variable efficacy of currently used drugs, however identified consistent efficacy of three novel drug classes: proteasome inhibitors, histone deacetylase inhibitors and cyclin-dependent kinase inhibitors. Gene expression of drug targets was highly reproducible comparing iALL cell lines to matched primary specimens. Histone deacetylase inhibitors, including romidepsin (ROM), enhanced the activity of a key component of iALL therapy, cytarabine (ARAC) in vitro and combined administration of ROM and ARAC to xenografted mice further reduced leukemia burden. Molecular studies showed that ROM reduces expression of cytidine deaminase, an enzyme involved in ARAC deactivation, and enhances the DNA damage–response to ARAC. In conclusion, we present a valuable resource for drug discovery, including the first systematic analysis of transcriptome reproducibility in vitro, and have identified ROM as a promising therapeutic for MLL-rearranged iALL.

Antileukemic Efficacy of BET Inhibitor in a Preclinical Mouse Model of MLL-AF4+ Infant ALL

“…We can speculate that these mechanisms might possibly explain the observed sensitization to prednisolone induced by I-BET151, although additional studies will be required to better address this hypothesis. HDACis were previously identified as active compounds against MLLrearranged cells (45) and their use in MLL-rearranged leukemias has shown antileukemic activity (46,47). For the first time in the present study, the efficacy of a combination treatment with BET and HDACis was reported for MLL-rearranged infant ALL.…”

“…The use of BET inhibitor in combination with HDACi has been already reported in several tumors including leukemia and the molecular mechanisms of their synergistic effect has been partially elucidated (16,17,49). HDACi redistributes the histone acetylation marks, mistargets BET proteins away from target active enhancers (49) and affects transcriptional elongation (46,49); while BET inhibitors abrogate transcription by selectively displacing BRD4 from super enhancers and interfering with the BRD4-mediated transcriptional pause release (31,50,51). Recently, novel BRD4/HDAC dual inhibitors were generated to successfully target a human MLL-AF4 þ AML cell line (52).…”

Recapitulation of human germline coding variation in an ultra-mutated infant leukemia

“…The study cohort consisted of ten infants diagnosed at Princess Margaret Hospital for Children (Perth), of which we have previously reported RNA-seq data for five patients 7 . Additional RNA-seq data was downloaded for 39 KMT2A-R iALL cases at diagnosis, six cases at relapse, six cases lacking the KMT2A-R (KMT2Agermline) and for pediatric KMT2A-R patients at diagnosis, comprising 10 AML cases, seven ALL cases and one undifferentiated case as reported previously by Andersson et al 5 (accession EGAS00001000246).…”

“…There were also ~40-fold increased number of indels in the dominant clone of the ultra-mutated sample (n=260) compared to typical cases (average = 6.6; range: [3][4][5][6][7][8][9] including 13 predicted to cause a frame-shift protein-coding truncation (Table 1; Supplementary Table S5). There were 2,420 exonic substitutions encoding 1,109 missense alleles and 12 stop-gain alleles ( Supplementary Table S5).…”

Romidepsin enhances the efficacy of cytarabine in vivo, revealing histone deacetylase inhibition as a promising therapeutic strategy for KMT2A-rearranged infant acute lymphoblastic leukemia

“…Romidepsin was shown to enhance the in vitro activity of cytarabine, a key component of infant ALL therapy, with an in vivo signal identified when combined with high-dose cytarabine. 3 In this study, we investigate the in vivo synergy between romidepsin and cytarabine, determine the in vivo toxicity of this combination, and further explore the effect of romidepsin on the DNA damageresponse to cytarabine. All in vivo experiments were approved by the Animal Ethics Committee, Telethon Kids Institute, Perth, Australia.…”