What Links the NAT10 RNA Acetyltransferase to Cancer and Metastasis?

Previous research from the laboratories of Ruhul Amin and Kent W. Hunter (National Cancer Institute, National Institutes of Health) demonstrated a link between genetic polymorphisms, which may influence gene expression rather than protein function, and metastatic potential (Hunter, 2015). Studies such as these prompted the discovery of multiple metastasis-susceptibility genes whose encoded proteins colocalize with the nuclear lamina or nuclear pore (Amin et al., 2021 and Alsarraj et al.), a location where the nuclear pore protein NUP210 facilitates mechanosensation from the extracellular microenvironment (Hayward et al.). Related studies suggest that the NAT10 (the only known enzyme that mediates the N4-acetylcytidine [ac4C] modification of a wide range of RNA species and proteins) also forms part of this mechanosensation machinery at the nuclear lamina (Alsarraj et al.). As such, a wide range of studies have implicated the acetylation activity of NAT10 in cancer development (Xie et al.) and metastasis (Liao et al., Zhang et al., Pan et al., and Ma et al.).

In a recent Molecular Cell study, researchers from the Amin and Hunter labs reported on their ongoing explorations of NAT10´s role in metastasis; fascinatingly, their new findings reveal a previously unknown mechanism: NAT10 modulates the activity of the p300/CBP histone acetyltransferases via the acetylation of chromatin-associated transfer RNAs to enhance metastatic potential through crosstalk with innate immune myeloid cells and the formation of a metastasis-promoting tumor microenvironment (Amin et al.). These findings suggest that NAT10 regulates gene enhancer activity in tumor cells and influences tumor-immune interactions, thereby contributing to metastatic potential.

The analysis of histone modification and transcriptomic profiles represents a key component of this fascinating new metastasis-associated study. Could Paired-Tag technology from Epigenome Technologies, which generates joint epigenetic and transcriptomic profiles at single-cell resolution and detects histone modifications and RNA transcripts in individual nuclei with efficiency comparable to single-nucleus RNA-seq/ChIP-seq assays, have provided additional information by supporting the analysis of histone acetylation and metastasis-associated gene expression in the same single cells?

NAT10 Controls an Acetylated Transfer RNA-p300/CBP-dependent Mechanism to Upregulate Metastasis-associated Gene Expression

The authors first employed mouse tumor models to demonstrate a significant decrease in metastasis following NAT10 depletion, confirming a role for NAT10’s acetyltransferase activity in metastatic progression. While studies had reported that NAT10 activity increases protein translation efficiency via mRNA ac4C-acetylation (Arango et al.), this new study failed to detect impaired translational efficiency in NAT10-depleted tumor cells and instead observed an adhesion defect similar to that observed with NUP210 depletion (Amin et al.). Fascinatingly, the authors discovered that NUP210, which facilitates mechanosensation from the extracellular microenvironment via the nuclear pore complex (Hayward et al.), interacted with NAT10 and may function via a metastasis-associated mechanosensitive pathway.

NAT10 depletion also decreased H3 and H4 acetylation (targets of the p300/CBP acetyltransferase) through an indirect mechanism: unexpectedly, NAT10 depletion prompted the upregulation of p300/CBP protein levels driven by increased protein acetylation but also altered their localization (increased colocalization with H3K9me3 and H3K27me3), which may have reduced their activity. Subsequent analyses revealed that NAT10 interacted with p300 (along with other nuclear pore-bound mechanosensitive proteins) at H3K27ac-/H4K20ac-modified gene enhancers, potentially regulating associated gene expression; however, NAT10 depletion altered p300 localization and disrupted enhancer organization/activity.

Studies have demonstrated that RNA binding to the p300 paralog CBP induces histone acetylation activity at gene enhancers (Bose et al.) and that chromatin-associated RNAs facilitate functional genomic interactions to regulate gene expression (Li and Fu); here, the authors discovered that NAT10 depletion increased p300 binding to chromatin-associated RNAs, which may explain the decrease in histone acetylation despite elevated p300/CBP protein levels in the absence of NAT10. In another unexpected finding, this study revealed that NAT10-mediated acetylation of specific chromatin-associated transfer RNAs may serve as an important modulator of p300/CBP histone acetyltransferase activity. As a consequence, the alterations induced by NAT10 loss led to significant transcriptional changes; RNA-sequencing analysis highlighted altered transcription of chemokine and cytokine genes and MYC targets, which can reshape the tumor immune microenvironment and impair neutrophil recruitment, thereby enhancing metastatic potential.

Overall, the authors define a mechanism in which increased tumor stiffness promotes NAT10 upregulation and the enhanced transcription of metastasis-associated genes via an acetylated transfer RNA-p300/CBP-dependent process. Therefore, NAT10 depletion reduces chromatin-associated transfer RNA acetylation, which alters p300 localization to disrupt gene enhancers and repress genes required for metastatic progression and myeloid cell recruitment, thereby creating a microenvironment that does not support metastasis.

NAT10, Mechanosensitivity, Microenvironments, and Metastasis: The Next Steps

The authors of this fascinating new study concluded their article by noting the need to next characterize NAT10´s role in regulating tumor-immune crosstalk and metastatic progression, and to consider the limitations of their study, which included a lack of direct evidence linking ac4C-modified chromatin-associated transfer RNAs to p300 chromatin occupancy. As noted previously, the implementation of Paired-Tag technology from Epigenome Technologies, which generates joint epigenetic and transcriptomic profiles at single-cell resolution and detects histone modifications and RNA transcripts in individual nuclei with efficiency comparable to single-nucleus RNA-seq/ChIP-seq assays, has the potential to provide deeper insight into studies such as these. What more could the simultaneous analysis of histone acetylation and metastasis-associated gene expression in the same single cell tell us about NAT10-mediated metastatic spread?