Emerging molecular subtypes and therapies in acute lymphoblastic leukemia

Integrative genetic and transcriptomic subtyping improves prognosis prediction in B-lineage acute lymphoblastic leukemia

Whole-transcriptomic sequencing (WTS) has remarkably advanced our understanding of B-lineage acute lymphoblastic leukemia (B-ALL), allowing for detailed gene expression profiling and discovery of novel therapeutically-relevant subtypes. The aim of this study was to evaluate the diagnostic and prognostic relevance of combining WTS with traditional genetic methods in risk-stratifying B-ALL. In a cohort of 394 patients (301 children and 93 adults), conventional techniques such as FISH, cytogenetics, and RT-PCR identified sentinel chromosomal abnormalities like BCR::ABL1, TCF3::PBX1, ETV6::RUNX1, and KMT2A-R (rearranged), and ploidy status. WTS was performed on selected 257 patients to identify subtypes such as Ph-like, DUX4-R, PAX5-altered (PAX5-ALT), MEF2D-R, BCL2-R, UBTF-R, PAX5 P80R, NUTM1-R, ZNF384-R, ZNF384-like, ETV6::RUNX1-like, IKZF1 N159Y, and HLF-R. We used a multi-pronged strategy to identify the borderline subtypes such as Ph-like, PAX5-ALT, and CRLF2 (non-Ph-like), by integrating gene expression signatures using tSNE, subtype defining mutations, gene fusions, and copy number assessments. Our integrated approach not only identifies prognostically relevant sentinel molecular subtypes but also increases subtype assignment in upto ∼95% of B-ALL patients. The pro-B immunophenotype was found to be more frequent in UBTF-R and MEF2D-R ALL. Ph-like ALL was associated with poor remission rates and higher minimal residual disease positivity, while DUX4-R showed favorable prognosis. We further categorized pediatric patients into three risk groups: Favorable (hyperdiploid, ETV6::RUNX1, DUX4-R), Poor (BCR::ABL1, Ph-like, KMT2A-R, TCF3::PBX1, iAMP21, and hypodiploid), and Intermediate (PAX5-ALT, PAX5 P80R, NUTM1-R, MEF2D-R, CRLF2 (non-Ph-like), UBTF-R, ZNF384-R, ZNF384-like, BCL2-R, IKZF1 N159Y, ETV6::RUNX1-like, and B-rest). EFS and OS were significantly associated with this risk stratification. In adults, Ph-like ALL showed worse prognosis, particularly, in BCR::ABL1 negative ALL patients. Among the DUX4-R B-ALL, those with IKZF1 deletion had worse EFS and OS. We also identified several novel gene rearrangements in different subtypes of B-ALL. Our study demonstrated that integrating WTS with traditional methods provides a comprehensive, accurate, cost-effective strategy for risk-assessment and treatment planning for B-ALL.

Bridging the Gap: Cost-Effective Strategies for Detecting Ph-Like B-Lineage ALL in Resource-Limited Settings

Acute lymphoblastic leukemia (ALL) is a complex hematologic disorder primarily affecting children, characterized by genetic mutations that disrupt normal lymphoid cell differentiation and promote abnormal proliferation. A particularly high-risk subtype, Philadelphia chromosome-like ALL (Ph-like ALL), mirrors the genetic profile of Philadelphia chromosome-positive (Ph-positive) ALL but lacks the BCR::ABL1 fusion gene. While Ph-like ALL has been extensively studied in high-income countries (HICs), it remains under-researched in low- and middle-income countries (LMICs), where resource limitations hinder accurate diagnosis and targeted therapy. This review addresses this gap by providing a comprehensive overview of the incidence, genetic landscape, and detection strategies for Ph-like ALL, with a special focus on LMICs. It underscores the prevalence of Ph-like ALL and its association with poor clinical outcomes, emphasizing the critical need for cost-effective diagnostic methodologies tailored to resource-constrained settings. Despite advancements in diagnostic technologies, such as whole gene expression profiling and next-generation sequencing, their high cost and extended turnaround times limit their feasibility in LMICs. Innovative methods, such as the PGIMER In-House Rapid and Cost-Effective (PHi-RACE) classifier, which employs real-time quantitative polymerase chain reaction (PCR), offer promising solutions by delivering high sensitivity and specificity at a significantly reduced cost. This approach is further complemented using fluorescence in situ hybridization (FISH) to characterize kinase alterations, enabling the identification of targeted therapies. This method addresses the urgent need for accessible diagnostic tools in LMICs, enabling early detection and personalized treatment planning. As the landscape of Ph-like ALL detection evolves, integrating low-cost, rapid-turnaround approaches holds significant promise for improving patient outcomes globally. This review aims to highlight the challenges and opportunities in diagnosing and treating Ph-like ALL in LMICs, fostering efforts towards more accessible and effective diagnostic strategies to enhance patient care and prognosis.

RNA-sequencing: A reliable tool to unveil transcriptional landscape of paediatric B-other acute lymphoblastic leukaemia

B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) comprises multiple subtypes characterized by different genetic alterations. With the use of current standard-of-care tests used in clinical practice, 20%-30% of the cases may not be classified into the main genetic subtypes and additional approaches are needed. These patients are grouped in the heterogeneous category B-other ALL. Transcriptome sequencing (RNA-seq) has allowed the identification of novel fusion genes and gene expression profiles that define new molecular subtypes. We present RNA-seq results integrated, in a real-world scenario, with clinical routine diagnostic data to identify new biomarkers and reclassify a cohort of 60 B-other ALL patients in the newly described genetic subtypes. Overall, 49 rearrangements were identified, including 32 different fusion genes in 41 B-other patients (68%). Moreover, we reported six novel rearrangements (IGK::PAX5, PAX5::IL1RAPL1, ETV6::KRT78, IGH::HIC1, IGH::MIR100HG and NKAIN4::PNPLA7). The integration of RNA-seq results with standard-of-care data allowed us to classify 72% of the patients (43/60) in 11 different subtypes, being DUX4 rearranged and PAX5alt the most represented subtypes. In summary, RNA-seq is a reliable tool for the identification of new emerging genetic subtypes contributing to a better genetic risk stratification of BCP-ALL paediatric patients on the path towards a more personalized medicine.

Deciphering IGH rearrangement complexity and detection strategies in acute lymphoblastic leukaemia

Acute lymphoblastic leukaemia is a highly heterogeneous malignancy characterised by various genomic alterations that influence disease progression and therapeutic outcomes. Gene fusions involving the immunoglobulin heavy chain gene represent a complex and diverse category. These fusions often result in enhancer hijacking, upregulation of partner proto-oncogenes and contribute to leukemogenesis. This review highlights the mechanisms underlying IGH gene fusions, the critical role they play in ALL pathogenesis, and current detection technologies.

Recurrent PAX5::ZCCHC7 rearrangement in B-cell acute lymphoblastic leukemia

The PAX5 (paired box 5) gene encodes a transcription factor that plays a critical role in B-cell development. PAX5 rearrangement is a recurrent abnormality seen in about 1.0-2.5% of B-cell acute lymphoblastic leukemia (B-ALL) cases. In this study, we presented 3 cases of B-ALL harboring PAX5::ZCCHC7 rearrangement. We subsequently reviewed the literature and identified 45 additional B-ALL cases with PAX5::ZCCHC7. Our data showed that the majority of B-ALL patients with PAX5::ZCCHC7 were observed in various subtypes of B-ALL, including BCR::ABL1-like, BCR::ABL1, ETV6::RUNX1 and others. In B-ALL, PAX5::ZCCHC7 was always co-occur with other subtype-defining rearrangements, which as the sole abnormality in only 8 patients, with the remaining 34 patients harboring CRLF2, JAK2, TCF3 or other rearrangements. In PAX5::ZCCHC7, the PAX5 breakpoints are mainly between exon 1 and 2 (30/51). As a result, nearly all PAX5 protein domains are lost in PAX5::ZCCHC7, suggesting that the PAX5::ZCCHC7 seems to disrupt PAX5 similarly to a PAX5 deletion. In summary, the PAX5::ZCCHC7 is a recurrent genetic aberration in B-ALL and seems to act as an additional genetic abnormality of subtype-defining aberration. Whether the PAX5::ZCCHC7 could act as a leukemia-initiating event or not needs further investigation.

BRD4 degraders may effectively counteract therapeutic resistance of leukemic stem cells in AML and ALL

Acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) are life-threatening hematopoietic malignancies characterized by clonal expansion of leukemic blasts in the bone marrow and peripheral blood. The epigenetic reader BRD4 and its downstream effector MYC have recently been identified as potential drug targets in human AML and ALL. We compared anti-leukemic efficacies of the small-molecule BET inhibitor JQ1 and the recently developed BRD4 degraders dBET1 and dBET6 in AML and ALL cells. JQ1, dBET1, and dBET6 were found to suppress growth and viability in all AML and ALL cell lines examined as well as in primary patient-derived AML and ALL cells, including CD34+/CD38- and CD34+/CD38+ leukemic stem and progenitor cells, independent of the type (variant) of leukemia or molecular driver expressed in leukemic cells. Moreover, we found that dBET6 overcomes osteoblast-induced drug resistance in AML and ALL cells, regardless of the type of leukemia or the drug applied. Most promising cooperative or even synergistic drug combination effects were seen with dBET6 and the FLT3 ITD blocker gilteritinib in FLT3 ITD-mutated AML cells, and with dBET6 and the multi-kinase blocker ponatinib in BCR::ABL1+ ALL cells. Finally, all BRD4-targeting drugs suppressed interferon-gamma- and tumor necrosis factor-alpha-induced expression of the resistance-related checkpoint antigen PD-L1 in AML and ALL cells, including LSC. In all assays examined, the BRD4 degrader dBET6 was a superior anti-leukemic drug compared with dBET1 and JQ1. Together, BRD4 degraders may provide enhanced inhibition of multiple mechanisms of therapy resistance in AML and ALL.

Linkage of cell division cycle 42 with clinical features, treatment response and survival in adult Philadelphia chromosome negative acute lymphoblastic leukemia

Cell division cycle 42 (CDC42) regulates the progression of leukemia via mediating proliferation and immune evasion of malignant cells. The study aimed to investigate the correlation of CDC42 with clinical features, treatment response, event-free survival (EFS) and overall survival (OS) in adult Philadelphia chromosome negative acute lymphoblastic leukemia (Ph- ALL) patients. CDC42 expression in bone marrow mononuclear cells was detected in 78 adult Ph- ALL patients and 10 donors using real-time reverse transcriptase-polymerase chain reaction. CDC42 was increased in adult Ph- ALL patients compared with donors (p < .001). Besides, elevated CDC42 was linked with pro-B ALL or early-T ALL (p = .038) and white blood cell (WBC) elevation at diagnosis (p = .025). Fifty (64.1%) and 23 (29.5%) patients had complete remission (CR) at 1 month and minimal residual disease (MRD) after CR, respectively. CDC42 was inversely associated with CR at 1 month (p = .034), but not MRD after CR (p = .066). Concerning survival, patients with CDC42 ≥ 3.310 (cut by median value in patients) showed a shortened EFS (p = .006) and OS (p = .036) compared to those with CDC42 < 3.310. In detail, patients with CDC42 ≥ 3.310 and CDC42 < 3.310 had 5-year EFS rate of 29.9% and 45.4%, and 5-year OS rate of 39.4% and 63.6%, correspondingly. Further multivariate Cox's regression analyses revealed that CDC42 ≥ 3.310 was independently related to shorter EFS (hazard ratio = 2.933, p = .005). Elevated CDC42 is related with pro-B ALL or early-T ALL, WBC elevation at diagnosis, unfavorable treatment response and worse survival in adult Ph- ALL patients.

The role of next-generation sequencing in hematologic malignancies

Next-generation sequencing (NGS) allows high-throughput detection of molecular changes in tumors. Over the past 15 years, NGS has rapidly evolved from a promising research tool to a core component of the clinical laboratory. Sequencing of tumor cells provides an important step in detecting somatic driver mutations that not only characterize the disease but also influence treatment decisions. For patients with hematologic malignancies, NGS has been used for accurate classification and diagnosis based on genetic alterations. The recently revised World Health Organization classification and the European LeukemiaNet recommendations for acute myeloid leukemia consider genetic abnormalities as a top priority for diagnosis, prognostication, monitoring of measurable residual disease, and treatment choice. This review aims to present the role and utility of various NGS approaches for the diagnosis, treatment, and follow-up of hemato-oncology patients.

IKZF1 Alterations and Therapeutic Targeting in B-Cell Acute Lymphoblastic Leukemia

IKZF1 encodes the transcription factor IKAROS, a zinc finger DNA-binding protein with a key role in lymphoid lineage development. IKAROS plays a critical role in the development of lineage-restricted mature lymphocytes. Deletions within IKZF1 in B-cell acute lymphoblastic leukemia (B-ALL) lead to a loss of normal IKAROS function, conferring leukemic stem cell properties, including self-renewal and subsequent uncontrolled growth. IKZF1 deletions are associated with treatment resistance and inferior outcomes. Early identification of IKZF1 deletions in B-ALL may inform the intensification of therapy and other potential treatment strategies to improve outcomes in this high-risk leukemia.