The KMT2A recombinome of acute leukemias in 2023

Establishment of a high-risk pediatric AML-derived cell line YCU-AML2 with genetic and metabolic vulnerabilities

The prognosis of acute myeloid leukemia (AML) with KMT2A::MLLT3 rearrangement and MECOM overexpression and/or KRAS mutation is dismal, and the optimal treatment strategy remains unclear. However, to the best of our knowledge, a suitable model (such as a cell line or its xenograft model) for research on this subtype has not been established. We established a novel AML cell line, YCU-AML2, and its xenograft model harboring KMT2A::MLLT3 rearrangement, MECOM overexpression, and KRAS G12A mutation. YCU-AML2 xenograft mice models developed AML and mimicked the clinical phenotype of the original patient. YCU-AML2 expressed high sensitivity to MEK inhibitors, such as trametinib and selumetinib. Moreover, YCU-AML2 also exhibited high sensitivity to L-asparaginase with glutaminase activity, perhaps because of its reliance on oxidative phosphorylation via glutaminolysis as its main energy source. We believe that the YCU-AML2 cell line and its xenograft model can serve as models to explore the molecular pathogenesis of high-risk AML with KMT2A::MLLT3 rearrangement, MECOM overexpression, and/or KRAS mutation and develop new treatment strategies.

Acute Myeloblastic Leukemia in a Child With Duchenne Muscular Dystrophy: A Novel Case and Brief Review of the Literature

We present the first documented case of acute myeloid leukemia in a patient with Duchenne muscular dystrophy (DMD). The patient also had a second degree relative that was an obligate carrier of DMD, who died of acute myeloid leukemia as an infant, meeting the criteria of hereditary hematologic malignancy syndrome. We discuss the challenges of managing cancer in the setting of DMD. We briefly review the literature investigating the possible role of dystrophin in carcinogenesis. Lastly, we discuss the possible etiologies of this patient's malignancy being from carcinogenic properties of dystrophin, a cancer-predisposing germline mutation within the family lineage, or genetically unrelated events. This adds to the list of reports of various malignancies in patients with DMD.

T-cell acute lymphoblastic leukaemia: subtype prevalence, clinical outcome, and emerging targeted treatments

T-cell Acute Lymphoblastic Leukaemia (T-ALL) is a high-risk hematological disease constituting ~20% of acute leukemias. To date, the only subtype recognized by the World Health Organization's International Consensus Classification is early T-cell precursor ALL. To improve clinical outcomes, several studies have investigated and defined T-ALL genomic subtypes within cohorts of varied ages and geographical locations. These studies have also utilized differing analysis methods including whole transcriptome, exome, or genome sequencing as well as immunophenotyping and cytogenetic testing. As a result, there are significant differences in reported subtypes as well as the frequency at which each occurs. The reported clinical outcomes for specific genomic alterations also depend on patient demographics and treatment protocols. This review synthesizes the data from four T-ALL genomic landscape studies establishing consensus and highlighting differences, details clinical outcomes for the most common genomic alterations observed in T-ALL patients, and proposes novel avenues for future investigation and treatment.

Is Enhancer Function Driven by Protein-Protein Interactions? From Bacteria to Leukemia

The precise regulation of the transcription of genes is essential for normal development and for the maintenance of life. Aberrant gene expression changes drive many human diseases. Despite this, we still do not completely understand how precise gene regulation is controlled in living systems. Enhancers are key regulatory elements that enable cells to specifically activate genes in response to environmental cues, or in a stage or tissue-specific manner. Any model of enhancer activity needs to answer two main questions: (1) how enhancers are able to identify and act on specific genes and (2) how enhancers influence transcription. To address these points, we first outline some of the basic principles that can be established from simpler prokaryotic systems, then discuss recent work on aberrant enhancer activity in leukemia. We argue that highly specific protein-protein interactions are a key driver of enhancer-promoter proximity, allowing enhancer-bound factors to directly act on RNA polymerase and activate transcription.

Effective Utilization of a Customized Targeted Hybrid Capture RNA Sequencing in the Routine Molecular Categorization of Adolescent and Adult B-Lineage Acute Lymphoblastic Leukemia: A Real-World Experience

INTRODUCTION

Recent World Health Organization (WHO) and International Consensus Classifications have introduced numerous molecular entities in B-lineage acute lymphoblastic leukemia (B-ALL), necessitating comprehensive genomic characterization by detecting gene fusions, expression, mutations, and exon deletions. While whole-genome plus transcriptome sequencing is the ideal strategy, it remains cost-prohibitive for routine use. This study reports a cost-effective and reasonably efficient alternate approach integrating a customized targeted hybrid capture RNA sequencing (RNAseq) into the routine workup.

METHODOLOGY

A total of 95 consecutive adolescent/adult B-ALL cases negative for common chimeric gene fusions (CGF) (BCR::ABL1, KMT2A::AFF1, TCF3::PBX1, and ETV6::RUNX1) were analyzed using a customized 69-gene targeted RNAseq panel. In total, three fusion detection pipelines, the Trinity Cancer Transcriptome Analysis Toolkit (CTAT) Mutations pipeline, and the Toblerone alignment tool were employed, and the results were compared with fluorescence in situ hybridization (FISH)/multiplex ligation-dependent probe amplification (MLPA) testing.

RESULTS

RNAseq identified fusions in 43% of cases (including BCR::ABL1-like: 15.8% and IGH::DUX4: 10.5%), demonstrating superior detection of cryptic intrachromosomal rearrangements. Somatic variants were detected in 30% of cases (including rat sarcoma (RAS) pathway and Janus kinase (JAK)-signal transducers and activators of transcription (STAT) variants in 18% and 5.3% respectively), and IKZF1 deletions were detected in 25% (77% concordance with MLPA). The integration of targeted RNAseq and comprehensive bioinformatic analysis with flow-cytometry-based ploidy analysis and FISH-based IGH rearrangements helped categorize 79% of common CGF-negative B-ALL. The BCR::ABL1/BCR::ABL1-like group showed a higher frequency of pathogenic IKZF1 deletions (50% versus 21.7%; p = 0.011), measurable residual disease (92% versus 51%; p = 0.009), and poorer overall survival (8.6 versus 22.8 months; p = 0.07).

DISCUSSION AND CONCLUSIONS

Effective utilization of RNAseq data by comprehensive bioinformatic analysis to test fusions, mutations, and deletions, supported by only minimal supplementary FISH testing, provides a practical, cost-effective solution for the molecular characterization of B-ALL in real-world scenarios until a single alternative and cost-effective test is available.

Next-generation sequencing RNA fusion panel for the diagnosis of haematological malignancies

Haematological malignancies are being increasingly defined by gene rearrangements, which have traditionally been detected by karyotype, fluorescent in situ hybridisation (FISH) or reverse-transcriptase polymerase chain reaction (RT-PCR). However, these traditional methods may miss cryptic gene rearrangements and are limited by the number of gene rearrangements screened at any one time. A next-generation sequencing (NGS) RNA fusion panel is an evolving technology that can identify multiple fusion transcripts in a single molecular assay, even without prior knowledge of breakpoints or fusion partners. We explored the utility of the Illumina TruSight RNA Fusion Panel for use in haematological malignancies by sequencing 30 peripheral blood or bone marrow aspirate samples. Secondary and tertiary analyses were performed using the Illumina DRAGEN RNA pipeline and PierianDx Clinical Genomics Workspace platform. Our RNA fusion panel was able to reliably detect known fusion transcripts, such as BCR::ABL1, ETV6::RUNX1 and KMT2A::AFF1, in acute lymphoblastic leukaemia (ALL), KMT2A::MLLT3, KMT2A::MLLT6, PML::RARA and CBFB::MYH11 in acute myeloid leukaemia (AML), and FIP1L1::PDGFRA in myeloid/lymphoid neoplasm with eosinophilia (MLN-Eo). In addition, it was able to detect rare KAT6A::CREBBP and CHIC2::ETV6 fusions, which could not be confirmed by traditional methods. The assay had a transcript limit of detection of approximately 5-10% of positive controls. These findings confirm the unique utility of the NGS-based RNA fusion panel as a diagnostic tool to identify gene rearrangements that drive haematological malignancies. It can identify novel and rare gene rearrangements to assist with diagnosis, prognostication and treatment decisions.

Unique Presentation of Autoinflammatory Disease-like Symptoms and Development of Leukemic Cell Lysis Pneumopathy in Childhood KMT2A::LASP1 -positive Acute Monocytic Leukemia

In the literature, long-term autoinflammatory disease (AID)-like symptoms are extremely rare in childhood acute leukemia cases. Here, we report a 14-month-old girl with KMT2A::LASP1 -positive acute monocytic leukemia diagnosed after a 7-month course of AID-like symptoms. KMT2A::LASP1 fusion was retrospectively detected in her bone marrow at the initial presentation of AID-like symptoms, suggesting the involvement of leukemia cells in her AID-like symptoms. Immediately after starting chemotherapy, the patient sequentially developed leukemic cell lysis pneumopathy (LCLP), which was successfully overcome by the continuation of chemotherapy under intensive respiratory support, thus suggesting a possible association of her AID-like symptoms with the development of LCLP.

KMT2A-CBL fusion gene in the first reported case of T-cell acute lymphoblastic leukemia associated with Wiedemann-Steiner syndrome

Wiedemann-Steiner syndrome (WSS) is a congenital malformation syndrome characterized by intellectual disability, developmental delay, and distinctive facial features, caused by germline mutations in the KMT2A gene. Despite the key role of KMT2A in hematopoiesis, leukemia has not been previously reported in WSS patients. This report presents the first documented case of acute lymphoblastic leukemia (ALL) in a WSS patient. A 16-year-old boy with developmental delay, distinct facial features, and genital abnormalities was diagnosed with WSS following the identification of a heterozygous frameshift mutation in KMT2A. At age 17, he developed T-cell ALL harboring the KMT2A-CBL fusion gene, of which only nine cases have been reported so far. cDNA sequence analysis of the KMT2A-CBL transcript at the site of the germline KMT2A pathogenic variant revealed a wild-type sequence, indicating that the KMT2A-CBL fusion occurred on the wild-type allele. While this observation suggests a potential cooperative role of the KMT2A-CBL chimeric gene and the germline KMT2A pathogenic mutation in leukemogenesis, the rarity of leukemia in WSS underscores the need for cautious interpretation. This case provides preliminary insights into a possible mechanism of leukemogenesis in WSS, but further studies are required to clarify the relationship between WSS and ALL.

Nidogen-1, a Player in KMT2A-Rearranged Pediatric Acute Myeloid Leukemia

Despite advances in outcome, one third of children with acute myeloid leukemia (AML) relapse, and less than half will achieve long-term survival. Relapse in AML has been shown to be driven in part by leukemic stem cells (LSCs), highlighting the unmet medical need to better characterize and target this therapy-resistant cell population. Micro-array profiling of pediatric AML subpopulations (LSCs and leukemic myeloblasts) and their healthy counterparts revealed nidogen-1 (NID1) as expressed in both leukemic subpopulations while absent in the hematopoietic stem cell. Using the TARGET dataset including pediatric AML patients (n = 1025), NID1 expression showed a correlation with worse event-free survival and KMT2A rearrangements. Drug response profiling of a NID1 knockdown model demonstrated differential sensitivity to HSP90 inhibition. RNA sequencing and gene set enrichment analysis between NID1high and NID1low phenotypes showed involvement of NID1 in mitochondrial metabolic pathways known to be enriched in LSCs. Altogether, this study highlights NID1 as a novel oncogene associated with worse EFS and metabolic LSC phenotype in AML. NID1 could serve as a biomarker and aid in further mapping LSCs to establish therapeutic strategies tackling the high relapse rates in pediatric AML.

Protocol for CRISPR-Cas9-mediated induction of KMT2A rearrangements in cell line and umbilical cord blood hematopoietic stem and progenitor cells

KMT2A rearrangements are associated with a poor clinical outcome in infant, pediatric, and adult acute lymphoblastic and myeloid leukemia. Here, we present a protocol to reconstruct chromosomal translocations with different partner genes of KMT2A in vitro. We describe steps for patient-specific single guide RNA (sgRNA) design, optimized sgRNA in vitro transcription, detailed purification of hematopoietic stem and progenitor cells (HSPCs) from umbilical cord blood (UCB), and CRISPR-Cas9 editing of the test cell line K562 as well as UCB HSPCs. The provided methodology is donor independent.

Fetal context conveys heritable protection against MLL-rearranged leukemia that depends on MLL3

MLL rearrangements ( MLL r) are the most common cause of congenital and infant leukemias. MLL r arise prior to birth and require few cooperating mutations for transformation, yet congenital leukemias are 10-fold less common than infant leukemias and >100-fold less common than childhood leukemias overall. This raises the question of whether mechanisms exist to suppress leukemic transformation during fetal life, thereby protecting the developing fetus from malignancy during a period of rapid hematopoietic progenitor expansion. Here, we use mouse models to show that fetal MLL::ENL exposure creates a heritable, leukemia-resistant state. MLL::ENL imposes a negative selective pressure on fetal hematopoietic progenitors. It leads to postnatal loss of self-renewal gene expression and enhanced myeloid differentiation that precludes transformation. These changes do not occur when MLL::ENL is induced shortly after birth, and transformation proceeds efficiently in this context. The fetal barrier to transformation is enforced by the histone methyltransferase MLL3. It can be overcome by cooperating mutations, such as Nras G12D , or through somatic or germline inactivation of MLL3. Heritable fetal protection against leukemic transformation may explain the low incidence of congenital leukemias in humans despite prenatal MLL rearrangement.

Monitoring the KMT2A gene post-chemotherapy independently predicts the relapse and survival risk after allogeneic haematopoietic stem cell transplantation

This study evaluated the kinetics of KMT2A-r during chemotherapy and its impact on allogeneic haematopoietic stem cell transplantation (allo-HSCT) outcomes. KMT2A-r was assessed post-induction (MRD1), after the first (MRD2) and second (MRD3) consolidations and pre-transplant (MRD4) in 52 patients with acute myeloid leukaemia (AML). KMT2A-r significantly decreased from diagnosis to MRD2 (p < 0.001 for diagnosis vs. MRD1; p = 0.019 for MRD1 vs. MRD2). The incidence of KMT2A-r negativity (57.5%) peaked at MRD2. KMT2A-r status at each time point significantly affected post-transplant outcomes. Cluster analysis identified four KMT2A-r kinetic profiles: persistently negative (-/-), turned negative at transplant (+/-), turned positive at transplant (-/+) and persistently positive (+/+). The (-/-) group had the best outcomes, with a cumulative incidence of relapse (CIR) of 13.0%, overall survival (OS) of 82.0% and leukaemia-free survival (LFS) of 81.7%. The (+/+) group had the worst prognosis, with a CIR of 58.8%, OS of 29.4% and LFS of 23.5%. KMT2A dynamics were an independent risk factor for CIR (Hazard ratio [HR] = 11.070, 95%CI 2.395-51.165, p = 0.002), LFS (HR = 9.316, 95%CI 2.656-32.668, p < 0.001) and OS (HR = 7.172, 95%CI 1.999-25.730, p = 0.003). In conclusion, KMT2A-r status after chemotherapy and its kinetics are significant HSCT prognostic indicators.

Cryptic KMT2A::AFDN Fusion Due to AFDN Insertion into KMT2A in a Patient with Acute Monoblastic Leukemia

BACKGROUND

KMT2A rearrangements occur in ~10% of acute myeloid leukemia (AML) cases and are critical for classification, risk stratification, and use of targeted therapy. However, insertions involving the KMT2A gene can evade detection using chromosomal analysis and/or fluorescence in situ hybridization (FISH).

METHODS

We present a case of a 22-year-old woman with acute monoblastic leukemia harboring a cryptic KMT2A::AFDN fusion identified by RNA sequencing. Initial FISH showed a 3' KMT2A deletion, while conventional karyotyping and the automated bioinformatic pipeline for optical genome mapping (OGM) did not identify the canonical translocation.

RESULTS

To resolve these discrepancies, metaphase KMT2A FISH (break-apart fusion probe) was performed to assess whether KMT2A was translocated to another chromosome. However, the results did not support this possibility. As the fusion signal remained on the normal chromosome 11, with the 5' KMT2A signal localized to the derivative chromosome 11. A subsequent manual review of the OGM data revealed a cryptic ~300 kb insertion of AFDN into the 3' region of KMT2A, reconciling the discrepancies between chromosomal analysis, FISH, and RNA fusion results.

CONCLUSIONS

This case highlights the importance of integrating multiple testing modalities with expert review when there is a discrepancy. Our findings emphasize the need for a comprehensive approach to genomic assessment to enhance diagnostic accuracy and guide therapeutic decision-making.

Pediatric AML: state of the Art and Future Directions

Pediatric acute myeloid leukemia (AML) is a heterogeneous and aggressive hematological malignancy. Despite advances in treatment, the survival rates remain unsatisfactory, emphasizing the need for innovative therapeutic approaches. This narrative review presents a comprehensive overview of the current approach and likely future directions for pediatric AML. The distinct genetic, epigenetic, and molecular features of pediatric AML contribute to its complex pathophysiology and impact on prognosis. Current treatment practices involve a multifaceted approach combining chemotherapy, molecularly targeted therapies, and hematopoietic stem cell transplantation. However, intensive treatment often leads to significant acute and long-term toxicity. Emerging strategies, including precision medicine, immunotherapy, and novel agents, hold promise for improving outcomes and minimizing adverse effects. Ongoing clinical trials are investigating the potential of these innovative approaches to transform pediatric AML care. By highlighting the evolving treatment paradigms and future perspectives, this review underscores the importance of continued research and development in pediatric AML to enhance the survival rates and quality of life of these young patients.

Antibody-Based and Other Novel Agents in Adult B-Cell Acute Lymphoblastic Leukemia

Despite notable progress in managing B-cell acute lymphoblastic leukemia (B-ALL) over recent decades, particularly in pediatric cohorts where the 5-year overall survival (OS) reaches 90%, outcomes for the 10-15% with relapsed and refractory disease remain unfavorable. This disparity is further accentuated in adults, where individuals over the age of 40 years undergoing aggressive multiagent chemotherapy continue to have lower survival rates. While the adoption of pediatric-inspired treatment protocols has enhanced complete remission (CR) rates among younger adults, 20-30% of these patients experience relapse, resulting in a subsequent 5-year OS rate of 40-50%. For relapsed B-ALL in adults, there is no universally accepted standard salvage therapy, and the median OS is short. The cornerstone of B-ALL treatment continues to be the utilization of combined cytotoxic chemotherapy regimens to maximize early and durable disease control. In this manuscript, we go beyond the multiagent chemotherapy medications developed prior to the 1980s and focus on the incorporation of antibody-based therapy for B-ALL with an eye on existing and upcoming approved indications for blinatumomab, inotuzumab ozogamicin, other monoclonal antibodies, and chimeric antigen receptor (CAR) T cell products in frontline and relapsed/refractory settings. In addition, we discuss emerging investigational therapies that harness the therapeutic vulnerabilities of the disease through targeting apoptosis, modifying epigenetics, and inhibiting the mTOR pathway.

Hemophagocytic Lymphohistiocytosis with Predominant T-Lymphocytes in Young Child: An Unusual Presentation of Evolving Acute Myeloid Leukemia

Background: Hemophagocytic lymphohistiocytosis (HLH) is an aggressive, life-threatening condition commonly observed in young children. Distinguishing primary HLH from secondary HLH, such as malignancy-associated HLH, can be challenging, potentially leading to misdiagnosis and inappropriate treatment. Case presentation: A 16-month-old female presented with fever, decreased appetite, and rhinorrhea. A review of the peripheral blood smear revealed anemia and leukopenia, with absolute neutropenia characterized by a high lymphocyte count (approximately 80% were T cells by flow cytometry). Flow cytometry was negative for immunophenotypically abnormal cells. Initially, the cytopenia was attributed to a viral infection. However, the cytopenia did not improve, and a bone marrow evaluation revealed evidence of HLH but no immunophenotypically abnormal population. An extensive work-up for HLH, including next-generation sequencing (NGS) and cytogenetic testing identified the KMT2A::MLLT3 fusion transcript, indicating malignancy-associated HLH in the setting of evolving leukemia. Because there was no increase in blasts or immunophenotypically abnormal cells, the diagnosis of leukemia could not be made at that time. The patient was closely monitored and, seven weeks later, was diagnosed with acute myeloid leukemia/acute monocytic leukemia. In addition to the KMT2A::MLLT3 fusion, pathogenic variants in the PTPN11 and FLT3 genes were detected by NGS. Conclusions: The presentation of evolving acute monocytic leukemia can be nonspecific, mimicking conditions such as HLH, without an initial increase in immature cells or monocytes. Maintaining a broad differential diagnosis and including comprehensive molecular genetic testing may facilitate early diagnosis and appropriate treatment.

Molecular Profiling Reveals Novel Gene Fusions and Genetic Markers for Refined Patient Stratification in Pediatric Acute Lymphoblastic Leukemia

Risk-adapted treatment protocols conferred remarkable improvement in the survival rates of pediatric acute lymphoblastic leukemia/lymphoma (ALL/LBL). Nevertheless, clinical management is still challenging in certain molecular subgroups and in the presence of alterations associated with an increased rate of relapse. In this study, disease-relevant genomic and transcriptomic profiles were established in a prospective, multicenter, real-world cohort involving 192 children diagnosed with ALL/LBL. Gene fusions were detected in 34.9% of B-ALL and 46.4% of T-ALL patients, with novel chimeric genes involving JAK2, KMT2A, PAX5, RUNX1, and NOTCH1, and with KMT2A-rearranged patients displaying the worst 3-year event-free survival (P = .019). Nonsynonymous mutations were uncovered in 74.9% of the analyzed patients, and pairwise scrutiny of genetic lesions revealed recurrent clonal selection mechanisms commonly converging on the same pathway (eg, Ras, JAK/STAT, and Notch) in individual patients. Investigation of matched diagnostic and relapse samples unraveled complex subclonal variegation, and mutations affecting the NT5C2, TP53, CDKN2A, and PIK3R1 genes, emerging at the time of relapse. TP53 and CREBBP mutations, even as subclonal aberrations, were associated with shorter 3-year event-free survival among all patients with B-ALL (TP53 mutant vs wild-type: P = .008, CREBBP mutant vs wild-type: P = .010), and notably, B-ALL patients showing no measurable residual disease on day 33 could be further stratified based on TP53 mutational status (P < .001). Our in-depth molecular characterization performed across all risk groups identified novel opportunities for molecularly targeted therapy in 55.9% of high-risk and 31.6% of standard/intermediate-risk patients.

Role of LEDGF/p75 (PSIP1) in oncogenesis. Insights in molecular mechanism and therapeutic potential

Aberrant gene expression due to dysfunction in proteins involved in transcriptional regulation is a hallmark of tumor development. Indeed, targeting transcriptional regulators represents an emerging approach in cancer therapeutics. Lens epithelium-derived growth factor (LEDGF/p75, PSIP1) is a co-transcriptional activator that tethers several proteins to the chromatin. LEDGF/p75 has been implicated in diseases such as HIV infection and KMT2A-rearranged leukemia. Notably, LEDGF/p75 is upregulated in various human cancers including prostate and breast cancer. In this review, we discuss the essential role of LEDGF/p75 in different malignancies and explore its mechanistic contribution to tumorigenesis revealing its potential as a therapeutic target for chemotherapy.

Prenatal and Perinatal Factors Associated with Infant Acute Lymphoblastic Leukaemia: A Scoping Review

OBJECTIVE

Acute lymphoblastic leukaemia (ALL) is the most frequent childhood cancer. Infant ALL (<1 year) is rare, but it captures a lot of interest due to its poor prognosis, especially in patients harbouring KMT2A rearrangements, which have been demonstrated to arise prenatally. However, epidemiological studies aimed at identifying specific risk factors in such cases are scarce, mainly due to sample-size limitations. We conducted a scoping review to elucidate the prenatal or perinatal factors associated with infant ALL.

METHODS

Original articles, letters, or conference abstracts published up to June 2022 were identified using the PubMed, Web of Science, and Embase databases, and 33 observational studies were selected.

RESULTS

The study reveals several well-established associations across the literature, such as maternal exposure to pesticides and high birth weight, and outlines suggestive associations, such as parental heavy smoking, parental use of several medications (e.g., dipyrone), and maternal exposure to air pollution during pregnancy.

CONCLUSIONS

This scoping review summarizes the few observational studies that have analysed the prenatal and perinatal risk factors for ALL in infants diagnosed before the age of 1 year. The results of this review highlight the lack of research into this specific age group, which merits further research.

MLL-AF4 upregulates 5-lipoxygenase expression in t(4;11) leukemia cells via the ALOX5 core promoter

5-Lipoxygenase (5-LO), encoded by the gene ALOX5, is implicated in several pathologies. As key enzyme in leukotriene biosynthesis, 5-LO plays a central role in inflammatory diseases, but the 5-LO pathway has also been linked to development of certain hematological and solid tumor malignancies. Of note, previous studies have shown that the leukemogenic fusion protein MLL-AF4 strongly increases ALOX5 gene promoter activity. Here, we investigate the upregulation of ALOX5 gene expression by MLL-AF4. Using reporter assays, we first identified the tandem GC box within the ALOX5 promotor sequence as the main target of MLL-AF4. Subsequently, we narrowed down the domains within the MLL-AF4 protein responsible for ALOX5 promoter activation. Our findings indicate that MLL-AF4 binds to the ALOX5 promoter via its CXXC domain and that the AF9ID, pSER and CHD domains redundantly activate transcriptional elongation. Knockdown of the MLL-AF4 gene in the human B cell line SEM revealed that MLL-AF4 is an inducer of ALOX5 gene expression in leukemic cells with lymphoid properties. Finally, we found that the MLL-AF4-related protein MLL-AF9, a driver of acute myeloid leukemia, similarly acts on the ALOX5 promoter. Taken together, we show that two prominent MLL fusion proteins are ALOX5 gene inducers in cells with lymphoid features.

Lactylation modulation identifies key biomarkers and therapeutic targets in KMT2A-rearranged AML

Acute Myeloid Leukemia (AML) with KMT2A rearrangements (KMT2Ar), found on chromosome 11q23, is often called KMT2A-rearranged AML (KMT2Ar-AML). This variant is highly aggressive, characterized by rapid disease progression and poor outcomes. Growing knowledge of epigenetic changes, especially lactylation, has opened new avenues for investigation and management of this subtype. Lactylation plays a significant role in cancer, inflammation, and tissue regeneration, but the underlying mechanisms are not yet fully understood. This research examined the influence of lactylation on gene expression within KMT2Ar-AML, initially identifying twelve notable lactylation-dependent differentially expressed genes (DEGs). Using advanced machine learning techniques, six key lactylation-associated genes (PFN1, S100A6, CBR1, LDHB, LGALS1, PRDX1) were identified as essential for prognostic evaluation and linked to relevant disease pathways. The study also suggested PI3K inhibitors and Pevonedistat as possible therapeutic options to modulate immune cell infiltration. Our findings confirm the critical role of lactylation in KMT2Ar-AML and identify six key genes that may serve as biomarkers for diagnosis and treatment. In addition to highlighting the need for further validation in clinical settings, these findings contribute to our understanding of KMT2Ar-AML's molecular mechanisms.

Application of RNA-Based Next-Generation Sequencing Fusion Assay for Hematological Malignancies

Recurrent fusions drive the pathogenesis of many hematological malignancies. Compared to routine cytogenetic/fluorescence in situ hybridization (FISH) studies, the RNA-based next-generation sequencing (NGS) fusion assay enables the identification of both known and novel fusions. In many cases, these recurrent fusions are crucial for diagnosis and are associated with prognosis, relapse prediction, and therapeutic options. The aim of this study is to investigate the application of the RNA-based NGS fusion assay in hematological malignancies. Our study included 3101 cases with available fusion results, and a fusion event was identified in 17.6% of cases. The discordant rate between the RNA-based NGS fusion assay and cytogenetic/FISH studies was 36.3%. Further analysis of discordant cases indicated that, compared to cytogenetic/FISH studies, the RNA-based NGS fusion assay significantly improved the identification of cryptic fusion genes, such as NUP98::NSD1, P2RY8::CRLF2, and KMT2A fusions involving different partners. Additionally, our study identified 24 novel fusions and 16 cases with the simultaneous presence of two fusions. These additional findings from the RNA-based NGS fusion assay resulted in improved risk stratification, disease targeting and monitoring. In conclusion, our study demonstrates the feasibility and utility of an RNA-based NGS fusion assay for patients with hematological malignancies, suggesting that it may be essential for the routine clinical workup of these patients.

Menin Inhibitors: New Targeted Therapies for Specific Genetic Subtypes of Difficult-to-Treat Acute Leukemias

Menin (MEN1) is a well-recognized powerful tumor promoter in acute leukemias (AL) with KMT2A rearrangements (KMT2Ar, also known as MLL) and mutant nucleophosmin 1 (NPM1m) acute myeloid leukemia (AML). MEN1 is essential for sustaining leukemic transformation due to its interaction with wild-type KMT2A and KMT2A fusion proteins, leading to the dysregulation of KMT2A target genes. MEN1 inhibitors (MIs), such as revumenib, ziftomenib, and other active small molecules, represent a promising new class of therapies currently under clinical development. By disrupting the MEN1-KMT2Ar complex, a group of proteins involved in chromatin remodeling, MIs induce apoptosis and differentiation AL expressing KMT2Ar or NPM1m AML. Phase I and II clinical trials have evaluated MIs as standalone treatments and combined them with other synergistic drugs, yielding promising results. These trials have demonstrated notable response rates with manageable toxicities. Among MIs, ziftomenib received orphan drug and breakthrough therapy designations from the European Medicines Agency in January 2024 and the Food and Drug Administration (FDA) in April 2024, respectively, for treating R/R patients with NPM1m AML. Additionally, in November 2024, the FDA approved revumenib for treating R/R patients with KMT2Ar-AL. This review focuses on the pathophysiology of MI-sensitive AL, primarily AML. It illustrates data from clinical trials and discusses the emergence of resistance mechanisms. In addition, we outline future directions for the use of MIs and emphasize the need for further research to fully realize the potential of these novel compounds, especially in the context of specific genetic subtypes of challenging AL.

Intensified conditioning containing decitabine versus standard myeloablative conditioning for adult patients with KMT2A-rearranged leukemia: a multicenter retrospective study

BACKGROUND

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is recommended for patients with KMT2A-rearranged (KMT2A-r) leukemia whereas relapse remains high. We aimed to determine whether intensified conditioning containing decitabine (Dec) could reduce relapse compared with standard myeloablative conditioning in adult patients with KMT2A-r leukemia.

METHODS

We performed a multicenter retrospective study at seven institutions in China. Eligible patients were aged 14 years or older at transplantation, had a diagnosis of KMT2A-r leukemia, and underwent the first allo-HSCT. Standard myeloablative conditioning regimens (standard group) included BuCy (busulfan 3.2 mg/kg/day on days -7 to -4; cyclophosphamide 60 mg/kg/day on days -3 to -2) and TBI-Cy (total body irradiation 4.5 Gy/day on days -5 to -4; Cy 60 mg/kg/day on days -3 to -2). Intensified conditioning regimens containing Dec (intensified group) consisted of Dec-BuCy (Dec 20 mg/m2/day on days -14 to -10; the same dose of BuCy) and Dec-TBI-Cy (Dec 20 mg/m2/day on days -10 to -6; the same dose of TBI-Cy).

RESULTS

Between April 2009 and December 2019, 218 patients were included in this study, of whom 105 were in the intensified group and 113 were in the standard group. The 3-year cumulative incidence of relapse was 17.6% and 34.5%, overall survival was 71.3% and 61.0%, disease-free survival was 70.1% and 56.0%, and non-relapse mortality was 12.3% and 9.5% in the intensified and standard groups, respectively (P = 0.001; P = 0.034; P = 0.005; P = 0.629). Subgroup analysis showed that the relapse rate of intensified conditioning was lower than that of standard conditioning in multiple subgroups, including different leukemia types, disease status at transplantation, high-risk cytogenetics and Bu-based regimens. There was no difference in regimen-related toxicity, engraftment, or graft-versus-host disease between the intensified and standard groups.

CONCLUSIONS

These results suggest that intensified conditioning containing Dec might be a better strategy than standard myeloablative conditioning for adult patients with KMT2A-r leukemia undergoing allo-HSCT.

Detection of KMT2A Partial Tandem Duplication by Optical Genome Mapping in Myeloid Neoplasms: Associated Cytogenetics, Gene Mutations, Treatment Responses, and Patient Outcomes

KMT2A partial tandem duplication (PTD) involves intragenic KMT2A duplications and has been associated with poorer prognosis. In this study, we evaluated KMT2A PTD in 1277 patients with hematological malignancies using optical genome mapping (OGM). KMT2A PTD was detected in 35 patients with acute myeloid leukemia (AML) (7%), 5 patients with myelodysplastic syndrome (MDS) (2.2%), and 5 patients with chronic myelomonocytic leukemia (CMML) (7.1%). The PTDs varied in size, region, and copy number. An Archer RNA fusion assay confirmed KMT2A PTD in all 25 patients tested: 15 spanning exons 2 to 8 and 10 spanning exons 2 to 10. Most patients exhibited a normal (n = 21) or non-complex (n = 20) karyotype. The most common chromosomal abnormalities included loss of 20q or 7q and trisomy 11/gain of 11q. All patients had gene mutations, with FLT3 ITD and DNMT3A prevalent in AML and DNMT3A and RUNX1 common in MDS and CMML. Among patients who received treatment and had at least one follow-up bone marrow evaluation, 82% of those with de novo AML achieved complete remission after initial induction chemotherapy, whereas 90% of patients with secondary or refractory/relapsed AML showed refractory or partial responses. All but one patient with MDS and CMML were refractory to therapy. We conclude that OGM is an effective tool for detecting KMT2A PTD. Neoplasms with KMT2A PTD frequently harbor gene mutations and display normal or non-complex karyotypes. Patients with KMT2A PTD are generally refractory to conventional therapy, except for de novo AML.

Unveiling the Complexity of KMT2A Rearrangements in Acute Myeloid Leukemias with Optical Genome Mapping

Background:KMT2A rearrangements are major genetic entities in the classification of acute myeloid leukemias (AMLs), but their diverse and frequently cryptic nature makes their detection and characterization challenging. Karyotypic anomalies at the KMT2A locus and/or abnormal KMT2A Fluorescence in situ hybridization (FISH) results strongly indicate a KMT2A fusion, but the identification of the translocation partner gene often requires further investigation. KMT2A partial tandem duplications (PTDs), on the other hand, are undetectable by standard cytogenetics methods. Methods: We herein report the optical genome mapping (OGM) analysis of 38 AML samples: 12 cryptic/hard-to-characterize KMT2A fusions, 20 KMT2A-PTDs and 6 cases with no KMT2A anomaly. Results: In all the fusion cases, the rearrangement between 5'KMT2A and the 3'partner gene was identified as a translocation t(v;11q23.3)(v;118479068), and the analysis of co-occurring variants elucidated the formation of the rearrangement. The KMT2A variants detected in the KMT2A-PTD cases were surprisingly diverse. Combined with RNAseq data, OGM analysis identified 9 distinct in-frame KMT2A-PTD variants among the 20 cases analyzed. Conclusions: With the clinical development of menin inhibitors for the treatment of patients with KMT2A-rearranged acute leukemias, the characterization of these rearrangements is of utmost importance. Our results suggest that OGM is a promising tool for accurate genetic diagnosis in this context.

Progress Toward Epigenetic Targeted Therapies for Childhood Cancer

Among the most significant discoveries from cancer genomics efforts has been the critical role of epigenetic dysregulation in cancer development and progression. Studies across diverse cancer types have revealed frequent mutations in genes encoding epigenetic regulators, alterations in DNA methylation and histone modifications, and a dramatic reorganization of chromatin structure. Epigenetic changes are especially relevant to pediatric cancers, which are often characterized by a low rate of genetic mutations. The inherent reversibility of epigenetic lesions has led to an intense interest in the development of epigenetic targeted therapies. Additionally, the recent appreciation of the interplay between the epigenome and immune regulation has sparked interest in combination therapies and synergistic immunotherapy approaches. Further, the recent appreciation of epigenetic variability as a driving force in cancer evolution has suggested new roles for epigenetic therapies in limiting plasticity and resistance. Here, we review recent progress and emerging directions in the development of epigenetic targeted therapeutics and their promise across the landscape of childhood cancers.

Pretransplant MRD detection of fusion transcripts is strongly prognostic in KMT2A-rearranged acute myeloid leukemia

ABSTRACT

Pretransplant detection of KMT2Ar measurable residual disease ≥0.001% by quantitative polymerase chain reaction was associated with significantly inferior posttransplant survival (2-year relapse-free survival 17% vs 59%; P = .001) and increased 2-year cumulative incidence of relapse (75% vs 25%, P = .0004).

Transplant in ALL: who, when, and how?

Allogeneic hematopoietic stem cell transplantation (allo-HCT) remains a cornerstone in the treatment of high-risk acute lymphoblastic leukemia (ALL), yet optimal patient selection is challenging in the era of rapidly changing modern therapy. Refined molecular characterization allows for better risk assessment, sparing low-risk patients from allo-HCT toxicity while identifying those who may benefit from intensified approaches. Measurable residual disease (MRD) has emerged as a powerful predictor of relapse irrespective of treatment strategy, challenging the necessity of transplant in MRD-negative patients. Further, expanded donor options, particularly haploidentical transplantation coupled with reduced intensity conditioning, have extended the applicability of allo-HCT to a broader range of patients. Finally, immunotherapies and targeted treatments are increasingly integrated into both initial and relapsed treatment protocols yielding deep remission and allowing for successful transplant in patients with a history of advanced disease. In this review, we provide an overview of the contemporary role of transplant in adult patients with ALL, focusing on indications for allo-HCT in first remission, optimal sequencing of transplant with novel therapies, and advancements in donor selection and conditioning regimens.

Pediatric therapy-related hematologic neoplasms show enrichment for KMT2A rearrangement and lymphoblastic phenotype

In children, therapy-related hematologic neoplasms (t-HN) are uncommon. Many are driven by genetic events independent of clonal hematopoiesis. We sought to understand the clinical and genetic factors of pediatric t-HN in a large independent cohort. Fifty-six t-HN were retrospectively identified. Chromosome microarray, next-generation and/or RNA sequencing were performed. Patients had primary hematologic, solid, or central nervous system tumors. t-HN included myeloid (t-MN) and lymphoblastic (t-ALL) phenotypes. Approximately half of the cases harbored KMTA2A rearrangement (KMT2Ar). Among t-HN without KMT2Ar, genetic drivers were heterogeneous, including diverse fusions or aneuploidy. Approximately 18% harbored 17p deletions and/or TP53 mutations. EFS/OS was not associated with t-HN lineage or KMT2Ar, but HSCT was associated with improved EFS and OS. We detail one of the largest cohorts to date of pediatric t-HN, confirming frequent KMT2Ar and t-ALL.

Lessons learned from 20 years of preclinical testing in pediatric cancers

Programs for preclinical testing of targeted cancer agents in murine models of childhood cancers have been supported by the National Cancer Institute (NCI) since 2004. These programs were established to work collaboratively with industry partners to address the paucity of targeted agents for pediatric cancers compared with the large number of agents developed and approved for malignancies primarily affecting adults. The distinctive biology of pediatric cancers and the relatively small numbers of pediatric cancer patients are major challenges for pediatric oncology drug development. These factors are exacerbated by the division of cancers into multiple subtypes that are further sub-classified by their genomic properties. The imbalance between the large number of candidate agents and small patient populations requires careful prioritization of agents developed for adult cancers for clinical evaluation in children with cancer. The NCI-supported preclinical pediatric programs have published positive and negative results of efficacy testing for over 100 agents to aid the pediatric research community in identifying the most promising candidates to move forward for clinical testing in pediatric oncology. Here, we review and summarize lessons learned from two decades of experience with the design and execution of preclinical trials of antineoplastic agents in murine models of childhood cancers.

Synergistic Strategies for KMT2A-Rearranged Leukemias: Beyond Menin Inhibitor

KMT2A-rearranged leukemias are a highly aggressive subset of acute leukemia, characterized by poor prognosis and frequent relapses despite intensive treatment. Menin inhibitors, which target the critical KMT2A-menin interaction driving leukemogenesis, have shown promise in early clinical trials. However, resistance to these inhibitors, often driven by menin mutations or alternative oncogenic pathways, remains a significant challenge. This review explores combination therapies aimed at overcoming resistance and improving patient outcomes. Potential strategies include inhibiting DOT1L, a histone methyltransferase essential for KMT2A-driven transcription, and BRD4, a regulator of transcriptional super-enhancers. Additionally, targeting MYC, a key oncogene frequently upregulated in KMT2A-rearranged leukemia, offers another approach. Direct inhibition of KMT2A-fusion proteins and c-MYB, a transcription factor critical for leukemic stem cell maintenance, is also explored. By integrating these diverse strategies, we propose a comprehensive therapeutic paradigm that targets multiple points of the leukemic transcriptional and epigenetic network. These combination approaches aim to disrupt key oncogenic pathways, reduce resistance, and enhance treatment efficacy, ultimately providing more durable remissions and improved survival for patients with KMT2A-rearranged leukemias.

Patient-Specific Circulating Tumor DNA for Monitoring Response to Menin Inhibitor Treatment in Preclinical Models of Infant Leukemia

BACKGROUND

In infant KMT2A (MLL1)-rearranged (MLL-r) acute lymphoblastic leukemia (ALL), early relapse and treatment response are currently monitored through invasive repeated bone marrow (BM) biopsies. Circulating tumor DNA (ctDNA) in peripheral blood (PB) provides a minimally invasive alternative, allowing for more frequent disease monitoring. However, a poor understanding of ctDNA dynamics has hampered its clinical translation. We explored the predictive value of ctDNA for detecting minimal/measurable residual disease (MRD) and drug response in a patient-derived xenograft (PDX) model of infant MLL-r ALL.

METHODS

Immune-deficient mice engrafted with three MLL-r ALL PDXs were monitored for ctDNA levels before and after treatment with the menin inhibitor SNDX-50469.

RESULTS

The amount of ctDNA detected strongly correlated with leukemia burden during initial engraftment prior to drug treatment. However, following SNDX-50469 treatment, the leukemic burden assessed by either PB leukemia cells through flow cytometry or ctDNA levels through droplet digital polymerase chain reaction (ddPCR) was discrepant. This divergence could be attributed to the persistence of leukemia cells in the spleen and BM, highlighting the ability of ctDNA to reflect disease dynamics in key leukemia infiltration sites.

CONCLUSIONS

Notably, ctDNA analysis proved to be a superior predictor of MRD compared to PB assessment alone, especially in instances of low disease burden. These findings highlight the potential of ctDNA as a sensitive biomarker for monitoring treatment response and detecting MRD in infant MLL-r ALL.

Only Infant MLL-Rearranged Leukemia Is Susceptible to an Inhibition of Polo-like Kinase 1 (PLK-1) by Volasertib

MLL-rearranged (MLLr) leukemia is characterized by a poor prognosis. Depending on the cell of origin, it differs in the aggressiveness and therapy response. For instance, in adults, volasertib blocking Polo-like kinase 1 (PLK-1) exhibited limited success. Otherwise, PLK-1 characterizes an infant MLLr signature, indicating potential sensitivity. By using our CRISPR/Cas9 MLLr model in CD34+ cells from human cord blood (huCB) and bone marrow (huBM) mimicking the infant and adult patient diseases, we were able to shed light on this phenomenon. The PLK-1 mRNA level was significantly increased in our huCB compared to the huBM model, which was underpinned by analyzing infant and adult MLLr leukemia patients. Importantly, the expression levels correlated with a functional response. Volasertib induced a significant dose-dependent decrease in proliferation and cell cycle arrest, most pronounced in the infant model. Mechanistically, upon volasertib treatment, we uncovered negative feedback only in the huBM model by compensatory upregulation of PLK-1 and related genes like AURKA involved in mitosis. Importantly, the poor response could be overcome by a combinatorial strategy with alisertib, an Aurora kinase A inhibitor. Our study emphasizes the importance of considering the cell of origin in therapeutic decision-making and provides the rationale for evaluating volasertib and alisertib in MLLr leukemia.

A rare case of pediatric T-cell acute lymphoblastic leukemia with myeloid mimicry

Acute lymphoblastic leukemia (ALL) with granular blasts was historically referred to as "granular ALL", but this is not recognized as a distinct entity in the current WHO classification. This rare morphological feature is predominantly associated with a B-cell immunophenotype, while T-ALL with prominent cytoplasmic granules is extremely rare, with limited available genetic, molecular, and prognostic data. Here, we report a unique case of ALL in a 9-year-old girl. Initial blood tests revealed leukocytosis, and both peripheral blood and bone marrow morphology showed a high number of blasts with granular cytoplasm and bilobed nuclei. Immunophenotyping confirmed T-cell origin. The patient tested positive for KMT2A::AFDN, with WT1 overexpression, and NRAS and EZH2 mutations were detected by next-generation sequencing (NGS). Remarkably, the patient achieved complete remission after treatment and has shown no signs of relapse for nearly four years. Her favorable response to conventional therapy underscores the importance of molecular phenotyping in the treatment of this disease. The continued use of NGS to gather relevant molecular data is crucial for further understanding the molecular phenotype and prognosis of such atypical ALL cases.

How CBX proteins regulate normal and leukemic blood cells

Hematopoietic stem cell (HSC) fate decisions are dictated by epigenetic landscapes. The Polycomb Repressive Complex 1 (PRC1) represses genes that induce differentiation, thereby maintaining HSC self-renewal. Depending on which chromobox (CBX) protein (CBX2, CBX4, CBX6, CBX7, or CBX8) is part of the PRC1 complex, HSC fate decisions differ. Here, we review how this occurs. We describe how CBX proteins dictate age-related changes in HSCs and stimulate oncogenic HSC fate decisions, either as canonical PRC1 members or by alternative interactions, including non-epigenetic regulation. CBX2, CBX7, and CBX8 enhance leukemia progression. To target, reprogram, and kill leukemic cells, we suggest and describe multiple therapeutic strategies to interfere with the epigenetic functions of oncogenic CBX proteins. Future studies should clarify to what extent the non-epigenetic function of cytoplasmic CBX proteins is important for normal, aged, and leukemic blood cells.

Revumenib for patients with acute leukemia: a new tool for differentiation therapy

Treatment of acute leukemia is gradually moving away from a "one-size-fits-all" approach, as scientific and clinical advances expand the arsenal of available targeted therapies. One of the recent additions is the group of menin inhibitors; oral, selective, small molecules that disrupt the interaction between the chromatin adapter menin, and an epigenetic regulator, the lysine methyltransferase 2A (KMT2A) complex. Two susceptible leukemia subtypes have been identified: (i) acute myeloid leukemia with a mutation in nucleophosmin 1 (NPM1), and (ii) any acute leukemia, myeloid or lymphoid, with a translocation resulting in the rearrangement of KMT2A. These leukemias share a distinct genetic expression, maintained by the KMT2A-menin interaction. Together they account for approximately 40% of patients with acute myeloid leukemia and 10% of patients with acute lymphoblastic leukemia. This spotlight review follows the journey of revumenib, as a representative of menin inhibitors, from bench to bedside. It focuses on the pathophysiology of leukemias sensitive to menin inhibition, delineation of how this understanding led to targeted drug development, and data from clinical trials. The important discovery of resistance mechanisms is also explored, as well as future directions in the use of menin inhibitors for treating leukemia.

MLL oncoprotein levels influence leukemia lineage identities

Chromosomal translocations involving the mixed-lineage leukemia (MLL) locus generate potent oncogenic fusion proteins (oncoproteins) that disrupt regulation of developmental gene expression. By profiling the oncoprotein-target sites of 36 broadly representative MLL-rearranged leukemia samples, including three samples that underwent a lymphoid-to-myeloid lineage-switching event in response to therapy, we find the genomic enrichment of the oncoprotein is highly variable between samples and subject to dynamic regulation. At high levels of expression, the oncoproteins preferentially activate either an acute lymphoblastic leukemia (ALL) program, enriched for pro-B-cell genes, or an acute myeloid leukemia (AML) program, enriched for hematopoietic-stem-cell genes. The fusion-partner-specific-binding patterns over these gene sets are highly correlated with the prevalence of each mutation in ALL versus AML. In lineage-switching samples the oncoprotein levels are reduced and the oncoproteins preferentially activate granulocyte-monocyte progenitor (GMP) genes. In a sample that lineage switched during treatment with the menin inhibitor revumenib, the oncoprotein and menin are reduced to undetectable levels, but ENL, a transcriptional cofactor of the oncoprotein, persists on numerous oncoprotein-target loci, including genes in the GMP-like lineage-switching program. We propose MLL oncoproteins promote lineage-switching events through dynamic chromatin binding at lineage-specific target genes, and may support resistance to menin inhibitors through similar changes in chromatin occupancy.

Evaluation of whole genome sequencing utility in identifying driver alterations in cancer genome

In cancer genome analysis, identifying pathogenic alterations and assessing their effects on oncogenic processes is important. Although whole exome sequencing (WES) can effectively detect such changes, driver alterations could not be identified in 27.8% of the cases, according to a previous study. The objectives of the present study were to evaluate the utility of whole genome sequencing (WGS) and clarify its differences with WES in terms of driver alteration detection. For this purpose, WGS analysis was conducted on 177 driverless WES samples, selected from 5,480 fresh frozen samples derived from 5,140 Japanese patients with cancer. These samples were selected as primary tumor, both WES and transcriptome profiling were performed, estimated tumor content of ≥ 30%, and no driver alterations were identified by WES. WGS identified driver and likely driver alterations in 68.4 and 22.6% of the samples, respectively. The most frequent alteration type was oncogene amplification, followed by tumor suppressor gene deletion and small variants located outside the coding region. In the remaining 9.0% of samples, no such signals were identified; therefore, further investigations are required. The current study clearly demonstrated the role and utility of WGS in identifying genomic alterations that contribute to tumorigenesis.

Histone methyltransferase KMT2A: Developmental regulation to oncogenic transformation

Our current understanding of epigenetic regulation is deeply rooted in the founding contributions of Dr C. David Allis. In 2002, Allis and colleagues first characterized the lysine methyltransferase activity of the mammalian KMT2A (MLL1), a paradigm-shifting discovery that brings epigenetic dysregulation into focus for many human diseases that carry KMT2A mutations. This review will discuss the current understanding of the multifaceted roles of KMT2A in development and disease, which has paved the way for innovative and upcoming approaches to cancer therapy.

Menin inhibitors in pediatric acute leukemia: a comprehensive review and recommendations to accelerate progress in collaboration with adult leukemia and the international community

Aberrant expression of HOX and MEIS1 family genes, as seen in KMT2A-rearranged, NUP98-rearranged, or NPM1-mutated leukemias leads to arrested differentiation and leukemia development. HOX family genes are essential gatekeepers of physiologic hematopoiesis, and their expression is regulated by the interaction between KMT2A and menin. Menin inhibitors block this interaction, downregulate the abnormal expression of MEIS1 and other transcription factors and thereby release the differentiation block. Menin inhibitors show significant clinical efficacy against KMT2A-rearranged and NPM1-mutated acute leukemias, with promising potential to address unmet needs in various pediatric leukemia subtypes. In this collaborative initiative, pediatric and adult hematologists/oncologists, and stem cell transplant physicians have united their expertise to explore the potential of menin inhibitors in pediatric leukemia treatment internationally. Our efforts aim to provide a comprehensive clinical overview of menin inhibitors, integrating preclinical evidence and insights from ongoing global clinical trials. Additionally, we propose future international, inclusive, and efficient clinical trial designs, integrating pediatric populations in adult trials, to ensure broad access to this promising therapy for all children and adolescents with menin-dependent leukemias.

Recent Developments and Evolving Therapeutic Strategies in KMT2A-Rearranged Acute Leukemia

BACKGROUND

Rearrangements of the histone-lysine-N-methyltransferase (KMT2A), previously referred to as mixed-lineage leukemia (MLL), are among the most common chromosomal abnormalities in patients with acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), involving numerous different fusion partners. KMT2A-rearranged (KMT2A-r) leukemia is characterized by a rapid onset, aggressive progression, and significantly worse prognosis compared to non-KMT2A-r leukemias. Even with contemporary chemotherapeutic treatments and hematopoietic stem cell transplantations (HSCT), patients with KMT2A-r leukemia typically experience poor outcomes and limited responses to these therapies.

OBJECTIVES

This review aims to consolidate recent studies on the general gene characteristics and associated mechanisms of KMT2A-r acute leukemia, as well as the cytogenetics, immunophenotype, clinical presentation, and risk stratification of both KMT2A-r-AML and KMT2A-r-ALL. Particularly, the treatment targets in KMT2A-r acute leukemia are examined.

METHODS

A comprehensive review was carried out by systematically synthesizing existing literature on PubMed, using the combination of the keywords 'KMT2A-rearranged acute leukemia', 'lymphoblastic leukemia', 'myeloid leukemia', and 'therapy'. The available studies were screened for selection based on quality and relevance.

CONCLUSIONS

Studies indicate that KMT2A rearrangements are present in over 70% of infant leukemia cases, approximately 10% of adult AML cases, and numerous instances of secondary acute leukemias, making it a disease of critical concern to clinicians and researchers alike. The future of KMT2A-r acute leukemia research is characterized by an expanding knowledge of the disease's biology, with an emphasis on personalized therapies, immunotherapies, genomic advancements, and innovative therapeutic combinations. The overarching aim is to enhance patient outcomes, lessen the disease burden, and elevate the quality of life for those affected. Ongoing research and clinical trials in this area continue to offer promising opportunities for refining treatment strategies and improving patient prognosis.

Preclinical efficacy of the potent, selective menin-KMT2A inhibitor JNJ-75276617 (bleximenib) in KMT2A- and NPM1-altered leukemias

ABSTRACT

The interaction between menin and histone-lysine N-methyltransferase 2A (KMT2A) is a critical dependency for KMT2A- or nucleophosmin 1 (NPM1)-altered leukemias and an emerging opportunity for therapeutic development. JNJ-75276617 (bleximenib) is a novel, orally bioavailable, potent, and selective protein-protein interaction inhibitor of the binding between menin and KMT2A. In KMT2A-rearranged (KMT2A-r) and NPM1-mutant (NPM1c) acute myeloid leukemia (AML) cells, JNJ-75276617 inhibited the association of the menin-KMT2A complex with chromatin at target gene promoters, resulting in reduced expression of several menin-KMT2A target genes, including MEIS1 and FLT3. JNJ-75276617 displayed potent antiproliferative activity across several AML and acute lymphoblastic leukemia (ALL) cell lines and patient samples harboring KMT2A or NPM1 alterations in vitro. In xenograft models of AML and ALL, JNJ-75276617 reduced leukemic burden and provided a significant dose-dependent survival benefit accompanied by expression changes of menin-KMT2A target genes. JNJ-75276617 demonstrated synergistic effects with gilteritinib in vitro in AML cells harboring KMT2A-r. JNJ-75276617 further exhibited synergistic effects with venetoclax and azacitidine in AML cells bearing KMT2A-r in vitro, and significantly increased survival in mice. Interestingly, JNJ-75276617 showed potent antiproliferative activity in cell lines engineered with recently discovered mutations (MEN1M327I or MEN1T349M) that developed in patients refractory to the menin-KMT2A inhibitor revumenib. A cocrystal structure of menin in complex with JNJ-75276617 indicates a unique binding mode distinct from other menin-KMT2A inhibitors, including revumenib. JNJ-75276617 is being clinically investigated for acute leukemias harboring KMT2A or NPM1 alterations, as a monotherapy for relapsed/refractory acute leukemia (NCT04811560), or in combination with AML-directed therapies (NCT05453903).

Circular RNA in cancer

Over the past decade, circular RNA (circRNA) research has evolved into a bona fide research field shedding light on the functional consequence of this unique family of RNA molecules in cancer. Although the method of formation and the abundance of circRNAs can differ from their cognate linear mRNA, the spectrum of interacting partners and their resultant cellular functions in oncogenesis are analogous. However, with 10 times more diversity in circRNA variants compared with linear RNA variants, combined with their hyperstability in the cell, circRNAs are equipped to influence every stage of oncogenesis. This is an opportune time to address the breadth of circRNA in cancer focused on their spatiotemporal expression, mutations in biogenesis factors and contemporary functions through each stage of cancer. In this Review, we highlight examples of functional circRNAs in specific cancers, which satisfy critical criteria, including their physical co-association with the target and circRNA abundance at stoichiometrically valid quantities. These considerations are essential to develop strategies for the therapeutic exploitation of circRNAs as biomarkers and targeted anticancer agents.

Activating mutations remodel the chromatin accessibility landscape to drive distinct regulatory networks in KMT2A-rearranged acute leukemia

Activating FLT3 and RAS mutations commonly occur in leukemia with KMT2A-gene rearrangements (KMT2A-r). However, how these mutations cooperate with the KMT2A-r to remodel the epigenetic landscape is unknown. Using a retroviral acute myeloid leukemia (AML) mouse model driven by KMT2A::MLLT3, we show that FLT3 ITD , FLT3 N676K , and NRAS G12D remodeled the chromatin accessibility landscape and associated transcriptional networks. Although the activating mutations shared a common core of chromatin changes, each mutation exhibits unique profiles with most opened peaks associating with enhancers in intronic or intergenic regions. Specifically, FLT3 N676K and NRAS G12D rewired similar chromatin and transcriptional networks, distinct from those mediated by FLT3 ITD . Motif analysis uncovered a role for the AP-1 family of transcription factors in KMT2A::MLLT3 leukemia with FLT3 N676K and NRAS G12D , whereas Runx1 and Stat5a/Stat5b were active in the presence of FLT3 ITD . Furthermore, transcriptional programs linked to immune cell regulation were activated in KMT2A-r AML expressing NRAS G12D or FLT3 N676K , and the expression of NKG2D-ligands on KMT2A-r cells rendered them sensitive to CAR T cell-mediated killing. Human KMT2A-r AML cells could be pharmacologically sensitized to NKG2D-CAR T cells by treatment with the histone deacetylase inhibitor LBH589 (panobinostat) which caused upregulation of NKG2D-ligand levels. Co-treatment with LBH589 and NKG2D-CAR T cells enabled robust AML cell killing, and the strongest effect was observed for cells expressing NRAS G12D . Finally, the results were validated and extended to acute leukemia in infancy. Combined, activating mutations induced mutation-specific changes in the epigenetic landscape, leading to changes in transcriptional programs orchestrated by specific transcription factor networks.

Rearrangements involving 11q23.3/KMT2A in adult AML: mutational landscape and prognostic implications - a HARMONY study

Balanced rearrangements involving the KMT2A gene (KMT2Ar) are recurrent genetic abnormalities in acute myeloid leukemia (AML), but there is lack of consensus regarding the prognostic impact of different fusion partners. Moreover, prognostic implications of gene mutations co-occurring with KMT2Ar are not established. From the HARMONY AML database 205 KMT2Ar adult patients were selected, 185 of whom had mutational information by a panel-based next-generation sequencing analysis. Overall survival (OS) was similar across the different translocations, including t(9;11)(p21.3;q23.3)/KMT2A::MLLT3 (p = 0.756). However, independent prognostic factors for OS in intensively treated patients were age >60 years (HR 2.1, p = 0.001), secondary AML (HR 2.2, p = 0.043), DNMT3A-mut (HR 2.1, p = 0.047) and KRAS-mut (HR 2.0, p = 0.005). In the subset of patients with de novo AML < 60 years, KRAS and TP53 were the prognostically most relevant mutated genes, as patients with a mutation of any of those two genes had a lower complete remission rate (50% vs 86%, p < 0.001) and inferior OS (median 7 vs 30 months, p < 0.001). Allogeneic hematopoietic stem cell transplantation in first complete remission was able to improve OS (p = 0.003). Our study highlights the importance of the mutational patterns in adult KMT2Ar AML and provides new insights into more accurate prognostic stratification of these patients.

KMT2A Rearrangements in Leukemias: Molecular Aspects and Therapeutic Perspectives

KMT2A (alias: mixed-lineage leukemia [MLL]) gene mapping on chromosome 11q23 encodes the lysine-specific histone N-methyltransferase 2A and promotes transcription by inducing an open chromatin conformation. Numerous genomic breakpoints within the KMT2A gene have been reported in young children and adults with hematologic disorders and are present in up to 10% of acute leukemias. These rearrangements describe distinct features and worse prognosis depending on the fusion partner, characterized by chemotherapy resistance and high rates of relapse, with a progression-free survival of 30-40% and overall survival below 25%. Less intensive regimens are used in pediatric patients, while new combination therapies and targeted immunotherapeutic agents are being explored in adults. Beneficial therapeutic effects, and even cure, can be reached with hematopoietic stem cell transplantation, mainly in young children with dismal molecular lesions; however, delayed related toxicities represent a concern. Herein, we summarize the translocation partner genes and partial tandem duplications of the KMT2A gene, their molecular impact, clinical aspects, and novel targeted therapies.