Tanja A. Gruber

Summary: Three-dimensional genome organization shapes gene regulation during normal B-cell development, and its disruption contributes to the initiation and progression of B-cell acute lymphoblastic leukemia. Through multi-omic studies, Ghebrechristos and colleagues revealed that transcription factors, including ERG in ETV6::RUNX1 leukemia, remodel chromatin interactions to sustain oncogenic gene expression programs, identifying genome architecture as both a driver of leukemogenesis and a potential therapeutic vulnerability. See related article by Ghebrechristos et al., p. XX .

Relapse remains the leading cause of mortality in pediatric acute myeloid leukemia (AML), yet the genetic changes contributing to relapse remain incompletely defined. To address this gap, we performed whole-genome sequencing and targeted-capture sequencing on 39 diagnosis–relapse and 2 relapse–relapse pairs of pediatric AML. Mutational burden increased at relapse, largely reflecting spontaneous mutagenesis, whereas therapy-related signatures were rarely observed and only occasionally associated with pathogenic mutations. Although recurrently enriched mutations at relapse included those in FLT3 , WT1 , and TP53 , relapse-fated subclones were frequently marked only by non-pathogenic or non-coding variants. Longitudinal deep sequencing in eight patients showed rapid depletion of major clones after induction therapy, whereas subclones often displayed variable chemosensitivity. Relapse-specific mutations emerged only late or remained undetectable during remission, suggesting that clonal selection of pre-existing clones is the predominant mechanism of relapse. Transcriptome analysis of paired RNA sequencing data revealed no differentially expressed genes, but gene set enrichment analysis and CIBERSORT deconvolution in each pair uncovered heterogeneous trajectories to relapse. Although relapse is often attributed to the emergence of stem-like phenotypes, our data demonstrate that transcriptional evolution is more diverse: some cases acquired stem-like features, whereas others showed partial differentiation, which was confirmed by re-analysis of a public single cell RNA sequence dataset. These changes were largely constrained by baseline differentiation states at diagnosis. Together, our data indicate that pediatric AML relapse arises through selection of pre-existing clones with diverse trajectories, underscoring the need to target both stem-like and differentiated populations to achieve durable cures.

To study the mechanisms of relapse in KMT2A-rearranged (KMT2A-r) acute lymphoblastic (ALL) and acute myeloid leukemia (AML), we performed whole-genome and exome sequencing of infants and children with relapsed ALL/AML (n = 36), and longitudinal deep-sequencing of 257 samples in 30 patients. Somatic alterations in drug-response genes, most commonly in TP53 and IKZF1 (64%), were highly enriched in early relapse ALL (79%, 9-36 months after diagnosis), but rare in very early relapse ALL (KMT2A-r ALL and AML evade therapy differently and provide insights into the mechanisms of relapse in this highly lethal form of pediatric acute leukemia.

T-lineage acute lymphoblastic leukemia (ALL) is an aggressive cancer comprising diverse subtypes that are challenging to stratify using conventional immunophenotyping. To gain insights into subset-specific therapeutic vulnerabilities, we performed an integrative multiomics analysis of bone marrow samples from newly diagnosed T cell ALL, early T cell precursor ALL, and T/myeloid mixed phenotype acute leukemia. Leveraging cellular indexing of transcriptomes and epitopes in conjunction with T cell receptor sequencing, we identified a subset of patient samples characterized by activation of inflammatory and stem gene programs. These inflammatory T-lineage samples exhibited distinct biological features compared with other T-lineage ALL samples, including the production of proinflammatory cytokines, prevalence of mutations affecting cytokine signaling and chromatin remodeling, an altered immune microenvironment, and poor treatment responses. Moreover, we found that, although inflammatory T-lineage ALL samples were less sensitive to dexamethasone, they exhibited unique sensitivity to a BCL-2 inhibitor, venetoclax. To facilitate classification of patients with T-lineage ALL, we developed a computational inflammatory gene signature scoring system, which stratified patients and was associated with disease prognosis in three additional patient cohorts. By identifying a high-risk T-lineage ALL subtype on the basis of an inflammatory score, our study provides a framework for targeted therapeutic approaches for these challenging-to-treat cancers.

CBFA2T3-GLIS2 is a fusion oncogene found in pediatric acute megakaryoblastic leukemia that is associated with a poor prognosis. We establish a model of CBFA2T3-GLIS2 driven acute megakaryoblastic leukemia that allows the distinction of fusion specific changes from those that reflect the megakaryoblast lineage of this leukemia. Using this model, we map fusion genome wide binding that in turn imparts the characteristic transcriptional signature. A network of transcription factor genes bound and upregulated by the fusion are found to have downstream effects that result in dysregulated signaling of developmental pathways including NOTCH, Hedgehog, TGFβ, and WNT. Transcriptional regulation is mediated by homo-dimerization and binding of the ETO transcription factor through the nervy homology region 2. Loss of nerve homology region 2 abrogated the development of leukemia, leading to downregulation of JAK/STAT, Hedgehog, and NOTCH transcriptional signatures. These data contribute to the understanding of CBFA2T3-GLIS2 mediated leukemogenesis and identify potential therapeutic vulnerabilities for future studies.

A t(4;11) leukemia model established from CRISPR-engineered chromosomal translocations between the KMT2A and AFF1 genes recapitulate proteomic, epigenomic, and transcriptomic features of primary patient leukemias.