Decoding UBC9 SUMOylation to stratify Rhabdomyosarcoma and identify precision therapeutic vulnerabilities

Background

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children, with most cases occurring before age 10. While rare (~4.5 million cases/year globally), it is challenging to treat and regimens have remained broadly stagnant over the past two decades (e.g., vincristine, dactinomycin, and cyclophosphamide). Five-year survival for high-risk or metastatic groups remains below 30%, unchanged since the 1970s.¹ These treatments carry debilitating side effects; survivors frequently suffer skeletomuscular developmental problems, cardiac and renal issues, nerve damage and reduced fertility, drastically impacting quality and length of life. Precision molecular therapies, or agents able to radio- or chemosensitise tumours, could dramatically improve patient outcomes and quality of life.

The Small Ubiquitin-like Modifier (SUMO) is a dynamic, reversible post-translational modification essential for cellular homeostasis, stress response, and adaptation to environmental change. The SUMO system influences cancer-related pathways including cell cycle progression, apoptosis and DNA repair, and dysregulation has been linked to tumorigenesis in pancreatic, oesophageal, lung and breast cancers.² TAK-981 (Subasumstat), an inhibitor of SUMO-Activating Enzyme (SAE1), is currently being evaluated in six clinical trials, primarily for solid tumours.

SUMOylation is controlled through an enzymatic cascade: the SAE1/SAE2 heterodimer activates SUMO before transferring it to UBC9, which delivers SUMOylation to target proteins with E3 enzyme assistance (e.g., PIAS). DeSUMOylation is carried out by Sentrin/SUMO-specific proteases (SENPs).

Recent work in the Gastaldello lab has demonstrated elevated levels of SUMOylation, SAE1, UBC9, and SENP1/5 in RMS.² Inhibition of SAE1 using TAK-981 impaired growth and chemosensitised RMS cell lines, supporting the SUMO pathway as a therapeutic target and raising the possibility of SUMO-pathway proteins as RMS biomarkers.

The Calder lab utilises a high-throughput mRNA-barcoded-peptide screening platform (mRNA display) to identify high-affinity binders from a library of over a trillion macrocyclic peptides.³ These peptides have drug-like properties and high selectivity. Optimisation through medicinal chemistry enables their application as imaging agents or inhibitors of protein function. Recently, the Calder lab has developed the first selective macrocyclic peptide binders of deSUMOylating enzymes SENP1 and 2 (unpublished).

We hypothesise that disruption of the SUMOylation pathway with macrocyclic peptide inhibitors will enable the discovery of new routes to treatment of RMS. To test this hypothesis, we aim to:

1. Identify selective inhibitors of UBC9 driven SUMOylation.

   Conduct mRNA display screening against UBC9 to discover novel selective macrocyclic peptide inhibitors of SUMOylation.

2. Validate SUMOylation inhibition as a therapeutic strategy in RMS.

   Test our SENP1 macrocyclic peptide inhibitors and newly identified UBC9 inhibitory peptides in fusion-positive alveolar and fusion-negative embryonal RMS cell lines and RMS-derived cells, assessing their ability to reduce or abolish key cancer features, including proliferation and invasion.

3. Define the molecular mechanisms of action.

   Characterise the downstream effects of targeting different SUMO-modulating enzymes using proteomics and targeted RT-qPCR to identify affected pathways and potential biomarkers of response.

4. Evaluate therapeutic efficacy and treatment sensitisation.

   Determine whether SUMOylation inhibition can attenuate or abolish malignant RMS phenotypes and enhance chemo- or radiosensitivity in both 2D cultures and hypoxic 3D spheroid models, including in combination with standard-of-care treatments.

5. Establish broader applicability to other solid cancers.

   Evaluate the most promising SUMOylation inhibitors across panels of molecularly characterised pancreatic, lung oesophageal and breast cancer models where SUMOylation has been linked to tumorigenesis.

This highly interdisciplinary project offers a broad experience in chemical, cellular and molecular biology as well as in genetics and oncology. The student will be primarily based at the Institute of Regeneration and Repair, with full access to School of Chemistry resources, and will spend time at the Institute for Genetics and Cancer and the Karolinska Institutet to progress the later aims of the project.

References: 

1 - https://doi.org/10.1158/1538-7445.AM2023-SY23-03

2 - https://doi.org/10.1007/s13402-024-00956-4

3 - https://doi.org/10.1007/s11010-025-05336-6

4 - https://doi.org/10.1038/s42004-024-01388-9