Clonal evolution and hierarchy in myeloid malignancies

Network-based clustering unveils interconnected landscapes of genomic and clinical features across myeloid malignancies

Myeloid malignancies exhibit considerable heterogeneity with overlapping clinical and genetic features among subtypes. We present a data-driven approach that integrates mutational features and clinical covariates at diagnosis within networks of their probabilistic relationships, enabling the discovery of patient subgroups. A key strength is its ability to include presumed causal directions in the edges linking clinical and mutational features, and account for them aptly in the clustering. In a cohort of 1323 patients, we identify subgroups that outperform established risk classifications in prognostic accuracy. Our approach generalises well to unseen cohorts with classification based on our subgroups similarly offering advantages in predicting prognosis. Our findings suggest that mutational patterns are often shared across myeloid malignancies, with distinct subtypes potentially representing evolutionary stages en route to leukemia. With pancancer TCGA data, we observe that our modelling framework extends naturally to other cancer types while still offering improvements in subgroup discovery.

From Chemotherapy to Targeted Therapy: Unraveling Resistance in Acute Myeloid Leukemia Through Genetic and Non-Genetic Insights

Acute myeloid leukemia (AML) is a devastating disease characterized by extensive inter-patient and intra-patient heterogeneity. Despite the introduction of intensive chemotherapy in the 1970s as the standard treatment, the development of mechanism-based targeted therapies since 2017 has been broadening the therapeutic landscape. However, both chemotherapy and targeted therapies continue to face the challenges of primary and secondary resistance. This review summarizes the mechanisms underlying resistance to chemotherapy and targeted therapies in AML and discusses the opportunities and challenges brought by the transition from chemotherapy to precision medicine.

Molecular Genetic Analysis of Bone Marrow Core Biopsy as an Alternative or Adjunct to Bone Marrow Aspirate and/or Peripheral Blood in Hematologic Myeloid Neoplasms

Background: The diagnosis of hematologic neoplasms is usually based on a synopsis of the peripheral blood (PB) and bone marrow findings. Morphology continues to be the cornerstone, but genetic analysis plays an increasingly important role. In routine workup, molecular genetic analysis is performed from a bone marrow aspirate (BMA). In the event of inadequate aspiration, PB is used. Not infrequently, however, PB only partially represents the disease. In this situation, molecular genetic analysis of formalin-fixed and paraffin-embedded (FFPE) bone marrow core biopsy (BMCB) could be a better alternative than PB. However, no systematic correlation of genetic findings from BMCB with results from BMA and PB has been reported. Methods: Therefore, BMCB obtained during routine diagnostics were subjected to post hoc molecular genetic analysis using next generation sequencing (NGS). The identified molecular genetic alterations were then compared with data within routine diagnostics of the corresponding BMA and/or PB. Results: In total, 29 BMCB and corresponding BMA samples were analyzed, and in 12/29 cases PB was additionally available. The analysis of BMCB and BMA showed identical results in 17 cases, but BMCB revealed a gain of information in 11, while in only 1 case, BMCB failed to identify the mutations in comparison to BMA. Conclusions: Despite the small numbers, molecular genetic analysis of bone marrow core biopsy using next generation sequencing could detect relevant additional gene mutations compared to bone marrow aspirate and/or peripheral blood.

Targeting myeloid cells for hematological malignancies: the present and future

Hematological malignancies are a diverse group of cancers that originate in the blood and bone marrow and are characterized by the abnormal proliferation and differentiation of hematopoietic cells. Myeloid blasts, which are derived from normal myeloid progenitors, play a central role in these diseases by disrupting hematopoiesis and driving disease progression. In addition, other myeloid cells, including tumor-associated macrophages and myeloid-derived suppressor cells, adapt dynamically to the tumor microenvironment, where they can promote immune evasion and resistance to treatment. This review explores the unique characteristics and pathogenic mechanisms of myeloid blasts, the immunosuppressive roles of myeloid cells, and their complex interactions within the TME. Furthermore, we highlight emerging therapeutic approaches targeting myeloid cells, focusing on strategies to reprogram their functions, inhibit their suppressive effects, or eliminate pathological populations altogether, as well as the latest preclinical and clinical trials advancing these approaches. By integrating insights from these studies, we aim to provide a comprehensive understanding of the roles of myeloid cells in hematological malignancies and their potential as therapeutic targets.

Somatic Genomic Alterations in Haematological Tumours Can Interfere With Accurate HLA and Chimerism Diagnostics

Tumour cells, which are often found in the peripheral blood of patients with acute leukaemia, may harbour multiple somatic alterations throughout the genome, including changes in the HLA region and short tandem repeat (STR) regions. We investigated whether such somatic alterations interfere with HLA and chimerism diagnostics conducted in preparation for an allogeneic haematopoietic stem cell transplantation (allo-HSCT). This study describes 10 patient-based cases for which laboratory diagnostics were performed prior to a possible stem cell transplant in the Maastricht University Medical Center. In three acute leukaemia patients, somatic alterations were detected within the HLA region in peripheral blood samples: one case showed a complete loss of an HLA haplotype, while two cases exhibited somatic mutations affecting a single HLA class I gene. Additionally, seven patients with haematological malignancies revealed somatic variations within the STR regions, indicated by the presence of a third allele or the partial or complete loss of an allele in pre-transplant peripheral blood samples. In all patients, these somatic variations were confirmed by repeating the tests using buccal swab samples from patients or samples from family members. Furthermore, our study demonstrated that somatic alterations within STR regions used for chimerism testing occurred in 6% of the 176 patients who received an allo-HSCT between 2017 and 2022. This study underscores the clinical relevance of detecting somatic alterations prior to allo-HSCT, as they may interfere with HLA and STR analysis, potentially leading to HLA mistyping or incorrect chimerism detection. Additionally, it highlights the frequency with which genetic changes in tumour cells can affect chimerism diagnostics. The findings emphasise the vital importance of selecting the appropriate sample source for typing purposes and considering the patient's karyotype when choosing STRs, especially when tumour cells are present in the peripheral blood of patients with haematological malignancies.

Leukemia aggressiveness is driven by chromatin remodeling and expression changes of core regulators

Molecular mechanisms driving clonal aggressiveness in leukemia are not fully understood. We tracked and analyzed MLL-rearranged leukemic clones independently evolving towards higher aggressiveness. More aggressive subclones lost their growth differential ex vivo but restored it upon secondary transplantation, suggesting molecular memory of aggressiveness. Development of aggressiveness was associated with clone-specific gradual modulation of chromatin states and expression levels across the genome, with a surprising preferential trend of reversing the earlier changes between normal and leukemic progenitors. To focus on the core aggressiveness program, we identified genes with consistent changes of expression and chromatin marks that were maintained in vivo and ex vivo in both clones. Overexpressing selected core genes (Smad1 as aggressiveness driver, Irx5 and Plag1 as suppressors) affected leukemic progenitor growth in the predicted way and had convergent downstream effects on central transcription factors and repressive epigenetic modifiers, suggesting a broader regulatory network of leukemic aggressiveness.

A View of Myeloid Transformation through the Hallmarks of Cancer

The development of myeloid malignancies is influenced by a range of cell-intrinsic and cell-extrinsic factors, which can be conceptualized using the hallmarks of cancer. Although many facets of myeloid transformation are similar to those in solid tumors, there are also notable differences. Unlike solid tumors, hematologic malignancies typically exhibit fewer genetic mutations, which have been well characterized. However, understanding the cell-extrinsic factors contributing to myeloid malignancies can be challenging due to the complex interactions in the hematopoietic microenvironment. Researchers need to focus on these intricate factors to prevent the early onset of myeloid transformation and develop appropriate interventions. Significance: Myeloid malignancies are common in the elderly, and acute myeloid leukemia has an adverse prognosis in older patients. Investigating cell-extrinsic factors influencing myeloid malignancies is crucial to developing approaches for preventing or halting disease progression and predicting clinical outcomes in patients with advanced disease. Whereas successful intervention may require targeting various mechanisms, understanding the contribution of each cell-extrinsic factor will help prioritize clinical targets.

Synergistic effects of the KDM4C inhibitor SD70 and the menin inhibitor MI-503 against MLL::AF9-driven acute myeloid leukaemia

MLL-rearranged (MLL-r) leukaemia is observed in approximately 10% of acute myeloid leukaemia (AML) and is associated with a relatively poor prognosis, highlighting the need for new treatment regimens. MLL fusion proteins produced by MLL rearrangements recruit KDM4C to mediate epigenetic reprogramming, which is required for the maintenance of MLL-r leukaemia. In this study, we used a combinatorial drug screen to selectively identify synergistic treatment partners for the KDM4C inhibitor SD70. The results showed that the drug combination of SD70 and MI-503, a potent menin-MLL inhibitor, induced synergistically enhanced apoptosis in MLL::AF9 leukaemia cells without affecting normal CD34+ cells. In vivo treatment with SD70 and MI-503 significantly prolonged survival in AML xenograft models. Differential gene expression analysis by RNA-seq following combined pharmacological inhibition of SD70 and MI-503 revealed changes in numerous genes, with MYC target genes being the most significantly downregulated. Taken together, these data provide preclinical evidence that the combination of SD70 and MI-503 is a potential dual-targeted therapy for MLL::AF9 AML.

Reduced Proteolipid Protein 2 promotes endoplasmic reticulum stress-related apoptosis and increases drug sensitivity in acute myeloid leukemia

BACKGROUND

The Proteolipid Protein 2 (PLP2), a protein in the Endoplasmic Reticulum (ER) membrane, has been reported to be highly expressed in various tumors. Previous studies have demonstrated that the reduced PLP2 can induce apoptosis and autophagy through ER stress-related pathways, leading to a decreased proliferation and aggressiveness. However, there is no research literature on the role of PLP2 in Acute Myeloid Leukemia (AML).

METHODS

PLP2 expression, clinical data, genetic mutations, and karyotype changes from GEO, TCGA, and timer2.0 databases were analyzed through the R packages. The possible functions and pathways of cells were explored through GO, KEGG, and GSEA enrichment analysis using the clusterProfiler R package. Immuno-infiltration analysis was conducted using the Cibersort algorithm and the Xcell R package. RT-PCR and western blot techniques were employed to identify the PLP2 expression, examine the knockdown effects in THP-1 cells, and assess the expression of genes associated with endoplasmic reticulum stress and apoptosis. Flow cytometry was utilized to determine the apoptosis and survival rates of different groups.

RESULTS

PLP2 expression was observed in different subsets of AML and other cancers. Enrichment analyses revealed that PLP2 was involved in various tumor-related biological processes, primarily apoptosis and lysosomal functions. Additionally, PLP2 expression showed a strong association with immune cell infiltration, particularly monocytes. In vitro, the knockdown of PLP2 enhanced endoplasmic reticulum stress-related apoptosis and increased drug sensitivity in THP-1 cells.

CONCLUSIONS

PLP2 could be a novel therapeutic target in AML, in addition, PLP2 is a potential endoplasmic reticulum stress regulatory gene in AML.