RBM39 as a Therapeutic Target in Acute Lymphoblastic Leukemia: Disruption of Cotranscriptional Splicing

Oncology Medicine Life Sciences Hematology
acute lymphoblastic leukemia RBM39 cotranscriptional splicing therapeutic target splicing factor

Research Summary

Potential of Targeting RBM39 in High-Risk Acute Lymphoblastic Leukemia (B-ALL)

Background Overview

Acute Lymphoblastic Leukemia (ALL) is a hematological malignancy commonly diagnosed in children and young adults. Despite high remission rates through frontline chemotherapies, the long-term survival rate for patients with relapsed/refractory B-ALL remains below 50%. Certain subtypes, such as Ph-like ALL, KMT2A-rearranged, or MEF2D fusion ALL, present an even poorer prognosis. Addressing relapsed/refractory B-ALL remains a major unmet need in hematologic oncology.

Aberrant RNA splicing has been widely observed in many cancers, including ALL, and has been recognized as a therapeutic target. RBM39 (RNA-binding motif protein 39), an RNA splicing-related protein, plays an essential role in maintaining tumor cell survival by promoting exon inclusion. While RBM39 has shown therapeutic potential in acute myeloid leukemia (AML), its specific role and mechanism in ALL remain underexplored. This study investigates the therapeutic potential of targeting RBM39 in relapsed/refractory B-ALL.

Paper Reference

The research was led by Professor John D. Crispino’s team at St. Jude Children’s Research Hospital, in collaboration with several international research institutions. This groundbreaking study was published in the premier hematological journal Blood on December 5, 2024, as a detailed original research article unveiling RBM39’s role and therapeutic potential in B-ALL.

Study Design and Experimental Workflow

This study employed a variety of in vitro, in vivo, and high-throughput data analysis techniques to comprehensively characterize RBM39’s mechanism in B-ALL and assess its therapeutic potential. The research was executed in four major steps:

1. Differential Splicing Analysis and Identification of RBM39 Poison Exon

Experimental Workflow:
The study began by comparing splicing patterns in normal CD19+ B-cells with those in B-ALL patient samples. It identified significantly enriched differential splicing events, notably the insertion of a poison exon in RBM39. DYRK1A inhibitors (e.g., EHT1610 and GNF2133) were found to drive this poison exon insertion via co-transcriptional splicing.

Key Findings:
Sashimi plots mapped the position and effect of the RBM39 poison exon. Poison exon inclusion activated nonsense-mediated mRNA decay (NMD), substantially reducing RBM39 protein levels.

2. Mechanistic Exploration of Poison Exon Inclusion

The study elucidated how DYRK1A inhibitors regulate splicing by influencing RNA Polymerase II (Pol II) phosphorylation and its interaction with the splicing factor SF3B1. Changes in Pol II serine-5 and serine-2 phosphorylation levels directly correlated with increased poison exon inclusion.

Using protein interactomics (IP-mass spec), SF3B1 was confirmed as a critical splicing regulator bound with phosphorylated Pol II. Disruption of Pol II phosphorylation or SF3B1 suppressed normal splicing events, favoring the poison exon inclusion in RBM39.

3. Dependency of Tumor Growth on RBM39

Using CRISPR/Cas9 and shRNA knockdown techniques, the research demonstrated RBM39’s critical role in B-ALL cell proliferation. RBM39 depletion resulted in significantly reduced growth, cell cycle arrest, and increased apoptosis.

In mouse xenograft models, RBM39 knockdown markedly inhibited tumor growth and prolonged survival. This dependency was particularly notable in high-risk subtypes (e.g., Ph-like and MEF2D fusion ALL).

4. Drug Development and Therapeutic Strategies to Target RBM39

The study validated RBM39 degraders, such as Indisulam (E7070) and E7820, which promote RBM39 protein ubiquitination via the DCAF15-mediated E3 ligase pathway. In patient-derived xenograft (PDX) models, E7820 exhibited potent anti-tumor activity, especially in the MEF2D fusion subtype.

Additionally, the study explored combination therapies using the DYRK1A inhibitor EHT1610 and the CDK9 inhibitor Dinaciclib, effectively inducing poison exon inclusion and RBM39 degradation. Significant anti-leukemia efficacy was achieved with this combination, with minimal toxicity to normal hematopoietic cells.

Major Findings and Conclusions

  1. Aberrant RBM39 Splicing:
    Inhibiting splicing regulators such as DYRK1A increased the inclusion of RBM39’s poison exon, activating the NMD pathway and reducing RBM39 protein levels.

  2. Pol II–SF3B1 Regulation:
    The association between RNA Pol II and SF3B1 was critical to controlling RBM39’s splicing. Disrupted Pol II phosphorylation significantly altered RBM39 splicing.

  3. Therapeutic Potential:
    RBM39 degradation agents (e.g., E7820) and splicing inhibitors showed strong anti-tumor effects, specifically in high-risk B-ALL subtypes.

Research Significance and Future Directions

This study provides a novel and effective approach to targeting relapsed/refractory B-ALL. RBM39 is not only identified as a key oncogenic regulator but has been extensively validated as a therapeutic target. Combining RBM39-targeting strategies with standard therapies has the potential to improve clinical outcomes significantly.

On a mechanistic level, the work deepens our understanding of RNA splicing and Pol II phosphorylation in cancer biology. It also sets the stage for exploring similar therapeutic targets in other malignancies. Future clinical trials investigating RBM39 degraders (e.g., E7820) and Pol II/splicing inhibitors for relapsed B-ALL patients are warranted.