Orthogonal proteogenomic analysis identifies the druggable PA2G4-MYC axis in 3q26 AML

Biochemistry Basic Medical Sciences Hematology Life Sciences Oncology Medicine
orthogonal proteogenomic acute myeloid leukemia EVI1 PA2G4 druggable target histone deacetylase inhibitors

Orthogonal Proteogenomic Analysis Identifies Druggable PA2G4-MYC Axis in 3q26 AML

Acute myeloid leukemia (AML) is a highly heterogeneous and aggressive malignancy. In particular, the 3q26 chromosomal abnormality subtype of AML has a complex pathogenic mechanism and lacks effective targeted therapies. To address this challenge, Matteo Marchesini and colleagues conducted a multi-dimensional proteogenomic analysis study aimed at unraveling the druggable potential in 3q26 AML. Their findings were published in the journal Nature Communications.

Research Background

Over the past two decades, rapid advances in molecular technologies have greatly improved the treatment prospects for acute myeloid leukemia patients. However, clinical progress remains limited for those with highly aggressive, rare subtypes, or relapsed and refractory diseases. For these AML subtypes, particularly those driven by aberrantly activated transcription factors (TFs), there are currently no effective, reproducible treatment methods. These TFs have long been considered “undruggable,” but recent developments have opened new avenues for their targeted therapy.

The 3q26 abnormal AML subtype is particularly deadly due to the overexpression of the EVI1/MECOM gene. These patients are typically resistant to conventional chemotherapy and have very low overall survival rates. Although small molecule, epigenetic, and metabolic inhibition strategies have shown potential in preclinical models, the multi-step optimization of EVI1 targeting is still ongoing.

The goal of this study was to identify an HDACi-responsive intermediary that can be targeted by drugs in 3q26 AML and to further elucidate the mechanism of HDACi-mediated EVI1 inhibition.

Research Source

This research was conducted by Matteo Marchesini, Andrea Gherli, Elisa Simoncini, and several other researchers from multiple research institutions, including the University of Parma. The paper was published in the journal Nature Communications in 2024.

Research Process

Experimental Design and Methods

The study employed a multi-step approach involving small molecule screening, gene expression profiling, and ultimately proteomics analysis to systematically identify the importance of the PA2G4-MYC axis in 3q26 AML.

  1. Small Molecule Screening:

    • Approximately 5,292 small molecule compounds, including natural derivatives, were screened.
    • AML cell lines Molm1 and UCSD/AML1 were treated, and their cell proliferation inhibition data were extracted.

  2. Gene Expression Profiling:

    • EVI1 expression was downregulated using RNA interference to redefine its transcriptional signature.
    • Public datasets (e.g., CMap) were used to identify small molecules and select compounds with potential for EVI1 targeted inhibition.

  3. Proteomics Analysis:

    • Rapid immunoprecipitation and mass spectrometry (RIME) were used to isolate and identify EVI1-associated chromatin protein complexes.
    • The role of PA2G4 in EVI1 signaling was elucidated.

Data and Results Analysis

The study results revealed the potent inhibitory effect of HDACi drugs on EVI1 and further established the potential of PA2G4 as an intervention target.

  1. Small Molecule Screening Results:

    • HDACi drugs (e.g., AR-42, Belinostat) were found to significantly inhibit the proliferation of EVI1-overexpressing AML cells.
    • In further counter-screening, HDACi drugs also exhibited significant effects on EVI1-overexpressing AML cell lines, indicating EVI1 sensitivity to HDACi drugs.

  2. EVI1 Transcriptional Signature Identification:

    • 1,428 EVI1-associated genes were redefined from the genome-wide expression profile.
    • In larger-scale chemical and gene perturbation datasets, HDACi drugs were repeatedly identified as top-ranking compounds associated with the EVI1 inhibition state.

  3. Proteomics Findings:

    • RIME identified EVI1-associated protein complexes, with PA2G4 emerging as a key interactor.
    • Small molecule inhibition of PA2G4 led to a significant decrease in EVI1 and MYC protein levels, suggesting a crucial role for PA2G4 in EVI1 and MYC signaling.

Clinical Validation

The study further validated the therapeutic effects of HDACi drugs in bone marrow samples from 3q26 AML patients and mouse models.

  1. Patient Sample Testing:

    • Under severe clinical conditions, HDACi drugs such as AR-42, Belinostat, and Entinostat exhibited significant inhibitory activity against AML cells in 2D and 3D model systems.
    • HDACi drugs significantly reduced the expression of EVI1 and its downstream target proteins, thereby activating cell apoptosis.

  2. Animal Model Testing:

    • In the 3q26 pdlx model, WS6 (a selective PA2G4 inhibitor) significantly inhibited AML cell growth.
    • In vivo experiments showed that WS6 achieved tumor suppression by reducing the expression of EVI1 and MYC.

Conclusions and Significance

Scientific and Application Value

  1. Scientific Value:

    • The study revealed the crucial role of the PA2G4-MYC axis in 3q26 AML, providing new insights into the pathological mechanisms.
    • The research established the potential of HDACi drugs in EVI1 targeted therapy, enriching the treatment strategies for AML.

  2. Application Value:

    • Identifying PA2G4 as a druggable target advances precision medicine for AML.
    • The study results support the application of HDACi drugs in combination therapy for 3q26 AML patients, providing new possibilities for clinical treatment.

Research Highlights

  1. Important Findings:

    • PA2G4 is a key regulator in EVI1 and MYC signaling, representing a novel and important finding in 3q26 AML.
    • HDACi drugs exhibited significant potency in inhibiting EVI1.

  2. Novelty:

    • A multi-dimensional approach combining genomics and proteomics analysis was employed, exploring new experimental and theoretical frameworks for AML treatment.
    • The study results not only bring new hope for AML treatment but also provide insights for the treatment of other related cancers.

The research findings provide a theoretical basis for precision therapy in 3q26 AML patients and pave the way for future research in related fields.