Meyling Cheok

Acute myeloid leukemia (AML) is a complex hematologic malignancy with multiple disease subgroups defined by somatic mutations and heterogeneous outcomes. Although genome-wide association studies (GWAS) have identified a small number of common genetic variants influencing AML risk, the heritable component of this disease outside of familial susceptibility remains largely undefined. Here, we perform a meta-analysis of 4 published GWAS plus 2 new GWAS, totaling 4710 AML cases and 12 938 controls. We identify a new genome-wide significant risk locus for pan-AML at 2p23.3 (rs4665765; P = 1.35 × 10−8; EFR3B, POMC, DNMT3A, and DNAJC27), which also significantly associates with patient survival (P = 6.09 × 10−3). Our analysis also identifies 3 new genome-wide significant risk loci for disease subgroups, including AML with deletions of chromosome 5 and/or 7 at 1q23.3 (rs12078864; P = 7.0 × 10−10; DUSP23) and cytogenetically complex AML at 2q33.3 (rs12988876; P = 3.28 × 10−8; PARD3B) and 2p21 (rs79918355; P = 1.60 × 10−9; EPCAM). We also investigated loci previously associated with the risk of clonal hematopoiesis (CH) or CH of indeterminate potential and identified several variants associated with the risk of AML. Our results further inform on AML etiology and demonstrate the existence of disease subgroup specific risk loci.

Relapse remains the leading cause of mortality in acute myeloid leukemia (AML), largely due to the persistence of therapy-resistant leukemia stem cells (LSCs). However, surface determinants that sustain LSC function and disease aggressiveness remain incompletely defined. Here, we identify the tetraspanin CD81 as a regulator of LSC function, progression and treatment resistance in AML. Analysis of retrospective patient cohorts revealed that high CD81 surface expression is associated with relapse and adverse clinical outcomes in non-core-binding factor AML. Functional studies demonstrated that elevated CD81 expression promotes chemoresistance and enhances leukemic engraftment in immunodeficient mouse models. In vivo gain- and loss-of-function approaches further established that CD81 drives increased leukemia burden and aggressive disease behavior. Notably, CD81 was enriched within LSC-containing subpopulations, where its expression supported LSC maintenance and resistance to chemotherapy. Mechanistically, CD81 promotes chemoresistance and leukemic aggressiveness through pathways linked to LAPTM4B-mediated STAT3 signaling and enhanced adhesion-dependent cellular interactions. These effects were accompanied by increased migration, invasion, and formation of filopodia-like membrane protrusions. Importantly, therapeutic immunotargeting of CD81 significantly reduced leukemic burden while exhibiting a manageable toxicity profile in preclinical models. Collectively, these findings establish CD81 as a clinically relevant surface marker associated with AML relapse and identify CD81-dependent signaling as a therapeutic vulnerability for targeting LSCs and preventing disease recurrence.

Loeys–Dietz syndrome (LDS) is an autosomal dominant connective-tissue disorder caused by genetic variants in TGF-β pathway genes, most often TGFBR1/2 . While pathogenic TGFBR2 mutations usually cluster in the kinase domain and disrupt SMAD signaling, the real challenge in accurate genetic testing is separating the variants that truly affect TGFBR2 function from the rare benign alterations that only look suspicious at first glance. Therefore, there is a pressing need to develop methods that can improve functional variant interpretation. Here, we describe and characterize the functional impact of a novel genetic variant in the TGFBR2 kinase domain (E431K), in a patient with the clinical diagnosis of syndromic genetic aortopathy. We assessed the structural and functional consequences of this variant using AI-driven molecular modelling and in vitro cell-based assays. A high-quality homology-based model of TGFBR2 was generated and computational mutagenesis based on the structural context and evolutionary conservation was used to forecast variant pathogenicity. Relative to wild type, the variant affects protein stability by disrupting intramolecular interactions and likely induces conformational changes that may affect kinase activity and thus TGF-β signalling. This was experimentally confirmed by showing abnormal protein level and alteration of canonical TGF-β pathway activation. Overall, our results establish that the E431K variant leads to aberrant TGF-β signalling and confirm the diagnosis of Loeys–Dietz syndrome type 2 in this patient.

Despite extensive research and intensive use of chemotherapies in clinics, the 5-year overall survival of acute myeloid leukemia (AML) patients does not exceed 20%. The clonal expansion of leukemic blasts leads to modifications of the bone marrow physical properties, including increased extracellular matrix stiffening, upregulation of intramedullary pressure and reduction of the space available for cells. These biomechanical modifications are speculated to alter therapeutic response and cause treatment resistance. To address this, we herein focused on the role of mechanotransduction pathways in AML. Analysis of primary AML samples or cell lines revealed that BMPR1B and TAZ/TEAD but not YAP levels were higher after patient relapse or in cells resistant to cytarabine or venetoclax. In addition, highly confined resident mesenchymal stem cells expressed higher levels of BMP4, which in turn specifically activated AML-resistant cells. In these cells, TAZ expression was associated with improved adhesion to microenvironmental components and increased intrinsic deformability. Finally, using a 3D human bone marrow-like model, we showed that targeting BMPR1B or TAZ/TEAD in combination with cytarabine impaired persistence of AML primary cells within the AML niche. Future therapeutic approaches could involve BMPR1B and/or TAZ/TEAD targeting in the context of AML patients refractory to chemotherapy or after relapse.

This paper studies the molecular effects on ex vivo drug response in pediatric acute myeloid leukemia (AML). We firstly estimate dose--response relationships through linear and mixed-effects models, capturing both patient-specific heterogeneity and drug-level effects. Then, drug identifiers are decomposed into curated molecular descriptors and their higher-order interactions, yielding a structured, interpretable representation of chemical properties. To handle the resulting high-dimensional system, we introduce a specialized graph-based drug decomposition and selection, enabling a computationally tractable estimation of the molecular effects on ex vivo drug response. This strategy uncovers the molecular features most strongly associated with cellular viability, providing a biologically grounded and transparent alternative to black-box predictive methods. By directly linking molecular structure to therapeutic outcomes, our framework supports a novel mathematical-programming-based drug-combination selection and cost-efficient compound prioritization in pre-clinical leukemia research.

Variability in genes involved in drug pharmacokinetics or drug response can be responsible for suboptimal treatment efficacy or predispose to adverse drug reactions. In addition to common genetic variations, large-scale sequencing studies have uncovered multiple rare genetic variants predicted to cause functional alterations in genes encoding proteins implicated in drug metabolism, transport and response. To understand the functional importance of rare genetic variants in DPYD, a pharmacogene whose alterations can cause severe toxicity in patients exposed to fluoropyrimidine-based regimens, massively parallel sequencing of the exonic regions and flanking splice junctions of the DPYD gene was performed in a series of nearly 3000 patients categorized according to pre-emptive DPD enzyme activity using the dihydrouracil/uracil ([UH₂]/[U]) plasma ratio as a surrogate marker of DPD activity. Our results underscore the importance of integrating next-generation sequencing-based pharmacogenomic interpretation into clinical decision making to minimize fluoropyrimidine-based chemotherapy toxicity without altering treatment efficacy.

Despite important progress over the last decade, acute myeloid leukemia (AML) is still associated with poor clinical outcome and novel efficient therapies ideally effective against AML stem cells (LSC), a major driver of leukemia initiation and progression, are urgently needed. In particular, targeting common AML-associated antigens at the stem and progenitor cell level represents an attractive therapeutic strategy to achieve deep long-term remissions and is currently the subject of intensive research efforts. In this study, we identified the tetraspanin CD81, a cell surface antigen frequently expressed on AML cells including LSC, as a new determinant of relapse and poor prognosis. CD81 expression was higher in AML cells compared to normal bone marrow cells, and more markedly expressed at relapse. We further showed that modulation of CD81 expression using gain- and loss-of-function approaches affected leukemia aggressiveness, tumor burden, LSC-homing and - xenoengraftment as well as mouse survival. Finally, anti-hCD81 monoclonal antibody- treatment combined with standard chemotherapy in mice with pre-established AML not only reduced leukemia burden but also prolonged relapse-free and overall survival. Collectively, these results identified a new efficient and safe pharmacological strategy for targeting LSC, opening up novel therapeutic avenues to improve AML outcome. Key points CD81 expression in AML including LSC is a new determinant of aggressive disease and poor prognosis. Anti-hCD81 monoclonal antibody-treatment of AML xenografts reduced leukemia burden and improved survival rates.

Whether the LSC17 gene expression can improve risk stratification in the context of next generation sequencing–based risk stratification and measurable residual disease (MRD) in patients with intensively treated AML has not been explored. We analyzed LSC17 in 504 adult patients prospectively treated in the ALFA-0702 trial. RUNX1 or TP53 mutations were associated with higher LSC1 scores while CEBPA and NPM1 mutations were associated with lower scores. Patients with high LSC17 scores had a lower rate of complete response (CR) in a multivariable analysis (odds ratio, 0.41; P = .0007), accounting for European LeukemiaNet 2022 (ELN22), age, and white blood cell count (WBC). LSC17-high status was associated with shorter overall survival (OS) (3-year OS: 70.0% vs 52.7% in patients with LSC17-low status; P < .0001). In a multivariable analysis considering ELN22, age, and WBC, patients with LSC17-high status had shorter disease-free survival (DFS) (hazard ratio [HR], 1.36; P = .048) than those with LSC17-low status. In 123 patients with NPM1-mutated AML in CR, LSC17-high status predicted poorer DFS (HR, 2.34; P = .01), independent of age, WBC, ELN22 risk, and NPM1-MRD. LSC-low status and negative NPM1-MRD identified a subset comprising 48% of patients with mutated NPM1 with a 3-year OS from CR of 93.1% compared with 60.7% in those with LSC17-high status and/or positive NPM1-MRD (P = .0001). Overall, LSC17 assessment refines genetic risk stratification in adult patients with AML treated intensively. Combined with MRD, LSC17 identifies a subset of patients with NPM1-mutated AML with excellent clinical outcome.