Identifying the mechanism that detoxifies toxic modified nucleosides

RNA involved in protein synthesis based on genetic information undergoes various chemical modifications in the body, and its functions and underlying mechanisms are actively being studied. While it is known that modified nucleosides^*1 are produced upon RNA degradation, their functions and metabolic pathways have remained unclear.

In this study, three types of modified nucleosides are found to be toxic to cells and re ultimately detoxified through stepwise processing by two enzymes. Furthermore, disruption of this metabolic pathway leads to abnormalities in glucose and lipid metabolism, resulting in dysfunction of intracellular organelles. This metabolic pathway is evolutionarily conserved across many species and may be closely associated with glucose and lipid metabolism in mammals.

*1 Nucleoside
A nucleoside is one of the building blocks of RNA, consisting of a sugar and a nitrogenous base. It undergoes various chemical modifications, such as methylation and acetylation.

Functions of modified nucleosides remain poorly understood

More than 150 types of RNA modifications have been identified. RNA modifications are involved in RNA function and stability. However, the functions of modified nucleosides that remain after RNA is degraded or metabolized have not been fully elucidated. This research group previously established a comprehensive method for detecting modified nucleosides in serum and urine, revealing the presence of diverse modified nucleosides in the body. Because some modified nucleosides were found to induce immune responses, they were considered not merely end products of metabolism. However, the functions of most modified nucleosides remain unknown.

Identification of toxic modified nucleosides and their metabolic pathways

Detoxification of three types of modified nucleosides

The research group first administered various modified nucleosides to cultured human cells and compared their effects on cell proliferation and survival. As a result, only three types of modified nucleosides—m⁶A (N6-methyladenosine), m⁶,⁶A (N6,N6-dimethyladenosine), and i⁶A (N6-isopentenyladenosine)—exhibited toxicity regardless of cell culture conditions or cell type.

Next, when examining the stability of modified nucleosides in the culture medium, most remained stable, whereas these three nucleosides disappeared within a short period. This suggested the existence of an intracellular metabolic pathway that degrades m⁶A, m⁶,⁶A, and i⁶A.

Further analysis focusing on metabolism revealed that, in the first step, adenosine kinase (ADK) phosphorylates these nucleosides, converting them to m⁶AMP, m⁶,⁶AMP, and i⁶AMP. In the second step, adenosine deaminase-like protein (ADAL) deaminates^*2 these monophosphates, converting them to inosine monophosphate (IMP), which is subsequently processed via the known purine metabolic pathway (Fig. 1).

*2 Deamination
A reaction in which an amino group is removed from a molecule. One of the mechanisms that regulates gene expression.

ADAL deficiency causes abnormalities in glucose and lipid metabolism

Although the function of ADK has been reported in previous studies, much about ADAL remains unclear. ADAL-deficient mice were generated and found to exhibit abnormal glucose metabolism and an inability to maintain normal blood glucose levels. This was attributed to the accumulation of the metabolic intermediates m6AMP, m6,6AMP, and i6AMP, which leads to decreased activity of AMP-activated protein kinase (AMPK)*3, a sensor of cellular energy status (Fig. 2 (right)).

In addition, in the livers of ADK-deficient mice, the expression of genes involved in lipid metabolism was significantly reduced. Analysis of lysosomes, one of the organelles involved in intracellular lipid metabolism, revealed that the toxic modified nucleosides m6A, m6,6A, and i6A caused lysosomal dysfunction (Fig. 2 (left)). Furthermore, treatment with compounds that stabilize lysosomes suppressed cell death, indicating that it was caused by organelle damage.

In this study, Associate Professor Akiko Ogawa discovered that toxic modified nucleosides exist in the body as metabolites of RNA modifications and demonstrated the pathways responsible for their detoxification. Professor Fan-Yan Wei, a pioneer in RNA modification and disease-related research, reported a new mechanism underlying modified nucleoside metabolism based on these findings.

*3 AMP-activated protein kinase (AMPK)
When cellular energy levels are low, AMPK is automatically activated. It inhibits energy-consuming processes and promotes energy-producing reactions.