Multi-omics analysis defines highly refractory RAS burdened immature subgroup of infant acute lymphoblastic leukemia

Abstract

KMT2A-rearranged infant acute lymphoblastic leukemia (ALL) represents the most refractory type of childhood leukemia. To uncover the molecular heterogeneity of this disease, we perform RNA sequencing, methylation array analysis, whole exome and targeted deep sequencing on 84 infants with KMT2A-rearranged leukemia. Our multi-omics clustering followed by single-sample and single-cell inference of hematopoietic differentiation establishes five robust integrative clusters (ICs) with different master transcription factors, fusion partners and corresponding stages of B-lymphopoietic and early hemato-endothelial development: IRX-type differentiated (IC1), IRX-type undifferentiated (IC2), HOXA-type MLLT1 (IC3), HOXA-type MLLT3 (IC4), and HOXA-type AFF1 (IC5). Importantly, our deep mutational analysis reveals that the number of RAS pathway mutations predicts prognosis and that the most refractory subgroup of IC2 possesses 100% frequency and the heaviest burden of RAS pathway mutations. Our findings highlight the previously under-appreciated intra- and inter-patient heterogeneity of KMT2A-rearranged infant ALL and provide a rationale for the future development of genomics-guided risk stratification and individualized therapy.

KMT2A oncoproteins induce epigenetic resistance to targeted therapies

“…The lineage identities and therapeutic responses of KMT2A r leukemias are highly heterogeneous 1,5,7,8 . To characterize the molecular basis of this heterogeneity we applied Automated CUT&RUN to profile the oncoprotein binding sites across 34 KMT2A r leukemia samples that span the age of onset and are representative of the diverse mutations and lineage subtypes that are observed in KMT2A r leukemias.…”

“…Advances in targeted immuno-therapies and pharmacological inhibitors have dramatically improved the treatment options for KMT2A r leukemias 5,6 . Despite sharing genetically related oncogenic lesions, KMT2A r leukemias show highly heterogeneous responses to therapeutic intervention 5,7,8 .…”

“…Mutations in Menin that block the interaction with Revumenib act as a genetic mechanism of resistance, however, some KMT2A r AMLs relapse in the absence of Menin mutations 14 , suggesting that an epigenetic resistance mechanism may also exist. Single cell RNA sequencing and chromatin profiling studies have identified considerable intra-tumoral heterogeneity in KMT2A r leukemia samples 8,15 , but why these leukemias display an unusual propensity for lineage switching remains unclear. Previously, we developed a high-throughput method for mapping the genome-wide binding sites of KMT2A oncoproteins in patient samples, and found the oncoprotein-target genes themselves are dynamically regulated 16 , suggesting the oncoproteins may contribute to the lineage plasticity and epigenetic resistance to targeted therapies.…”

Clustered regularly interspaced short palindromic repeats screens in pediatric tumours: A review

“…Other studies have shown that pediatric tumours are often stalled in their developmental programs related to their cell of origin, which could be translated to a developmental program specific sgRNA library to use in pediatric tumour models. 91,96 In particular for transductions of tumour source material or intricate organoid model systems, where cell numbers are often limited, a smaller sgRNA library would be of great benefit to study genetic dependencies.…”

A phase 2 trial of peri-operative avelumab and chemotherapy for locally advanced gastro-esophageal adenocarcinoma: Association of AGR2/AP-1 complex CD8 T-cells and M2-Tumour Associated Macrophages with treatment response

“…Based on these classi cations, the differential gene expression was calculated using the Seurat tool 'FindMarkers' using DESeq2 as the 'test.use' 56 . This methodology has been found to accurately identify differentially expressed genes in comparison with alternative exploratory tools and been used in multiple other exploratory studies of differential gene expression [57][58][59] . An average Log2 (fold change) >1 and an adjusted p value <0.05 were considered the cut-off criteria for differentially expressed genes.…”