Identification of Nonsense-Mediated Decay Inhibitors that Increase Expression of Truncated Proteins and Enhance Presentation of Tumor Neoantigens

Core Concepts

Inhibition of the nonsense-mediated decay (NMD) pathway using a novel SMG1 inhibitor, KVS0001, increases the expression of transcripts and proteins resulting from truncating mutations, leading to enhanced presentation of tumor-specific neoantigens on the cell surface.

Abstract

The authors developed a high-throughput screening assay to identify small molecule inhibitors of the nonsense-mediated decay (NMD) pathway. The screen revealed that disruption of the kinase SMG1's phosphorylation of UPF1 is a potent disruptor of NMD. This led the authors to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from truncating mutations both in vitro and in vivo.
Importantly, KVS0001 treatment concomitantly increased the presentation of immune-targetable HLA class I-associated peptides derived from NMD-downregulated proteins on the surface of cancer cells. The authors demonstrated that this enhanced neoantigen presentation could be targeted by a bispecific antibody, leading to increased T-cell activation and cancer cell killing.
In syngeneic mouse tumor models, treatment with KVS0001 slowed tumor growth in an immune-dependent manner, suggesting that inhibition of the NMD pathway can unveil previously hidden neoantigens and enhance anti-tumor immune responses.

Stats

"Mutant transcript levels increased 5 to 10-fold relative to untreated cells after treatment with the top hit compounds from the high-throughput screen."
"Treatment with LY3023414 increased the expression of the mutant allele in 42% and 67% of heterozygous, out-of-frame, indel mutations in NCI-H358 and LS180 cancer cell lines, respectively."
"Treatment with KVS0001 led to a 45 to 90 fold increase in the presentation of EXOC1 and RAB14 derived neoantigens, and a 2 fold increase in the ZDHHC16 derived neoantigen on the cell surface of NCI-H358 and LS180 cells."
"Treatment of syngeneic mouse tumor models (LLC and RENCA) with KVS0001 resulted in significant slowing of tumor growth in an immune-dependent manner."

Quotes

"Disruption of the nonsense-mediated decay pathway with a newly developed SMG1 inhibitor with in-vivo activity increases the expression of T-cell targetable cancer neoantigens resulting from truncating mutations."
"KVS0001 provides new opportunities for studying NMD and the diseases in which NMD plays a role, including cancer and inherited diseases."

Key Insights Distilled From

Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape

by Cook,A. L., ... at www.biorxiv.org 12-29-2023

https://www.biorxiv.org/content/10.1101/2023.12.28.573594v1

Deeper Inquiries

How might the use of NMD inhibitors like KVS0001 be extended beyond cancer treatment to prevent the onset of symptoms in patients with inherited diseases caused by truncating mutations?

Inherited diseases caused by truncating mutations, such as cystic fibrosis or β-thalassemia, result in the production of abnormal proteins that can lead to various health issues. NMD inhibitors like KVS0001 could potentially be used to prevent the onset of symptoms in patients with these conditions by allowing the expression of truncated mutant transcripts that are normally degraded by the NMD pathway. By inhibiting NMD, these inhibitors could increase the production of functional proteins from these mutant transcripts, potentially alleviating the symptoms associated with these inherited diseases. This approach could be particularly beneficial in pediatric syndromes where early intervention could prevent the progression of the disease.

What are the potential limitations or risks associated with long-term inhibition of the NMD pathway, given its important role in normal gene expression and development?

While NMD inhibitors like KVS0001 show promise in enhancing the expression of targetable cancer neoantigens and potentially treating certain diseases, there are important limitations and risks associated with long-term inhibition of the NMD pathway. The NMD pathway plays a crucial role in mRNA quality control and normal gene expression, ensuring the removal of aberrant transcripts and maintaining cellular homeostasis. Prolonged inhibition of NMD could lead to the accumulation of faulty transcripts, disrupting normal cellular functions and potentially causing cellular stress or dysfunction. This could result in unintended consequences such as the production of aberrant proteins, activation of stress response pathways, or interference with essential cellular processes. Additionally, since NMD is involved in the regulation of gene expression during development, long-term inhibition of this pathway may have detrimental effects on normal growth and differentiation processes. Therefore, careful consideration and monitoring of the potential off-target effects and risks associated with NMD inhibition are essential before considering its long-term use as a therapeutic strategy.

Could the insights gained from studying the NMD pathway and its modulation lead to the discovery of novel biomarkers or therapeutic targets beyond just enhancing neoantigen presentation?

Studying the NMD pathway and its modulation not only provides insights into enhancing neoantigen presentation for cancer immunotherapy but also opens up avenues for the discovery of novel biomarkers and therapeutic targets in various diseases. The dysregulation of the NMD pathway has been implicated in a wide range of conditions, including cancer, neurodegenerative disorders, and genetic diseases. By understanding the mechanisms of NMD and how it influences gene expression, researchers can identify specific biomarkers associated with NMD activity or dysfunction. These biomarkers could be utilized for diagnostic purposes, disease monitoring, or predicting treatment responses in patients. Furthermore, the identification of key regulators or components of the NMD pathway as potential therapeutic targets could lead to the development of novel drugs or interventions for various diseases beyond cancer. Targeting specific molecules involved in NMD modulation could offer new treatment strategies for conditions where NMD plays a critical role in pathogenesis, providing opportunities for precision medicine and personalized therapies.