Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. The translocation t(1;19), encoding the TCF3-PBX1 fusion, is associated with intermediate risk and central nervous system (CNS) infiltration at relapse. Using our previously generated TCF3-PBX1 conditional knock-in mice, we established a model to study relapsed clones after in vivo chemotherapy treatment, CNS infiltration, and clonal dynamic evolution of phenotypic diversity at the single cell-level using next-generation sequencing technologies and mass cytometry. Mice transplanted with TCF3-PBX1+ leukemia cells and treated with vehicle succumbed to disease, whereas 40% of treated mice with prednisolone or daunorubicin survived. Bulk and single-cell RNA sequencing of FACS-sorted GFP+ cells from TCF3-PBX1+ leukemias arising after chemotherapy treatment revealed that apoptosis, interleukin-, and TGFβ-signaling pathways were regulated in CNS-infiltrating leukemic cells. Across tissues, upregulation of the MYC signaling pathway was detected in persisting leukemic cells and its downregulation by BRD3/4 inhibition increased sensitivity to chemotherapy. In TCF3-PBX1+ leukemia cells collected after chemotherapy treatment, mass cytometry identified increased phosphorylation of STAT3/5 upon preBCR stimulation, which was susceptible to inhibition by the proteasome inhibitor bortezomib. In summary, we developed a TCF3-PBX1+ ALL mouse model and characterized relapsed disease after in vivo chemotherapy and cell phenotype dependence on microenvironment. Transcriptomics and phospho-proteomics revealed distinct pathways that may underlie chemotherapy resistance and might be suitable for pharmacological interventions in human ALL.
As a consequence of rapidly developing genetic technologies and advances in the understanding of the pathogenesis of acute myeloid leukemia (AML), the classification of AML has moved gradually from a morphologic and cytochemical-based system to one that is genetically defined. Recent molecular and genetic developments have been integrated into the diagnostic criteria for AML in the fifth edition of the World Health Organization (WHO) Classification of Haematolymphoid Tumours and the 2022 International Consensus Classification (ICC) of Myeloid Neoplasms and Acute Leukemias, expanding the list of genetically defined entities. In this review article, we use a case-based format describing the diagnostic workup, risk stratification, and possible treatment options to highlight the impact of the 2022 WHO and ICC classifications on clinical practice. We show that despite much commentary and anguish, there is a significant overlap between the two classifications. We further highlight the fact that even for entities with divergent nomenclature, such as TP53-mutated AML, the actual genetic lesion leads to convergent therapy.
The definition of high-risk (HR) multiple myeloma (MM) is still a matter of debate. We prospectively evaluated the HR detection using FISH in combination with SKY92 gene expression profiling in 258 MM patients (newly diagnosed [ND] MM: n = 109; relapsed/refractory [RR] MM: n = 149). HR SKY92 was significantly enriched in RRMM (57/121, 47.1%) compared with NDMM (17/95, 17.9%) (p < 0.0001). RRMM patients with HR SKY92 showed significantly shorter progression-free survival (PFS) (p < 0.0001) and overall survival (OS) (p < 0.0001) than SKY92 standard-risk (SR). In NDMM, HR SKY92 also indicated a significantly inferior PFS (p < 0.0001) in comparison with SR. We combined SKY92 with FISH (HR: t(4;14), del17p, +1q21 according to R2-ISS) in 181 patients (NDMM: n = 79; RRMM: n = 102). We found a discrepancy between both risk stratification systems, with only 49 (27.1%) patients being defined as HR by both SKY92 and FISH (“double HR”). In terms of survival outcomes, “double HR” presented a negative prognostic factor for PFS in both NDMM (p < 0.0001) and RRMM (p < 0.0001). Furthermore, “double-HR” patients showed the worst OS (p = 0.000 13) in RRMM. Additionally, whole genome sequencing (WGS) revealed CRBN mutation (n = 3) and bi-allelic events (mutation and/or deletion) in TP53 (n = 7) and TNFRSF17 (n = 1). Altogether, we provide the first prospective real-world evidence that the combination SKY92 and FISH (according to R2-ISS) identifies a subset of patients with ultra-HR MM, and WGS complements SKY92 and FISH in MM risk stratification.
Lower risk (LR) myelodysplastic syndromes (MDS) are heterogeneous hematopoietic stem and progenitor disorders caused by the accumulation of somatic mutations in various genes including epigenetic regulators that may produce convergent DNA methylation patterns driving specific gene expression profiles. The integration of genomic, epigenomic, and transcriptomic profiling has the potential to spotlight distinct LR-MDS categories on the basis of pathophysiological mechanisms. We performed a comprehensive study of somatic mutations and DNA methylation in a large and clinically well-annotated cohort of treatment-naive patients with LR-MDS at diagnosis from the EUMDS registry (ClinicalTrials.gov.NCT00600860). Unsupervised clustering analyses identified six clusters based on genetic profiling that concentrate into four clusters on the basis of genome-wide methylation profiling with significant overlap between the two clustering modes. The four methylation clusters showed distinct clinical and genetic features and distinct methylation landscape. All clusters shared hypermethylated enhancers enriched in binding motifs for ETS and bZIP (C/EBP) transcription factor families, involved in the regulation of myeloid cell differentiation. By contrast, one cluster gathering patients with early leukemic evolution exhibited a specific pattern of hypermethylated promoters and, distinctly from other clusters, the upregulation of AP-1 complex members FOS/FOSL2 together with the absence of hypermethylation of their binding motif at target gene enhancers, which is of relevance for leukemic initiation. Among MDS patients with lower-risk IPSS-M, this cluster displayed a significantly inferior overall survival (p < 0.0001). Our study showed that genetic and DNA methylation features of LR-MDS at early stages may refine risk stratification, therefore offering the frame for a precocious therapeutic intervention.