Decoding RNA modifications to unlock new treatments for AML Free

In this issue of Blood, Pauli et al¹ have identified and characterized a synthetic lethal interaction in acute myeloid leukemia (AML) between the loss of a specific mitochondrial transfer RNA (tRNA) modification and sensitivity to chemotherapy, specifically to cytarabine (AraC).

AML is a disease driven by a relatively limited repertoire of recurrent genetic mutations and chromosomal translocations. These DNA fingerprints regulate AML phenotype and clinical presentations, response to treatment and have helped to drive a revolution in targeted therapy through inhibitors of genes like FLT3 and IDH1/2. However, patient outcomes and disease heterogeneity are not purely driven by genetic factors, and clinical factors such as age, and nongenetic determinants of how a cell responds to stress can be important mediators of treatment resistance.^2,3 

Acute cellular responses to stress require dynamic regulation of the proteome, such as what can be achieved through modifications to messenger RNA (mRNA) due to their effects on translation efficiency. Accordingly, recent work has identified and characterized aberrant RNA modifications as critical determinants of normal and disease biology, including in AML. For example, the METTL3 methyltransferase catalyzes the deposition of N⁶-methyladenosine (m⁶A), the most common modification of mRNA, and has been shown to play an essential role in the maintenance of AML through effects on protein translation.⁴ Importantly, the effects of RNA modifications on translation extend beyond mRNA. Indeed tRNA, the key molecule responsible for decoding mRNA into amino acids, is the most extensively modified.

RNA in human cells and undergoes ∼11 to 13 site-specific and chemically specific modifications in every cell.^5,6 Recently, there has been renewed interest in understanding the impact of RNA regulators on human health and disease.

In this context, Pauli et al sought to identify regulators of RNA modifications in AML biology and response to treatment, beginning by screening 16 cancer cell lines with a bespoke genetic screen targeting all known writers, readers, and erasers of RNA modifications. This was followed by a secondary screen in 5 AML cell lines, to specifically evaluate targets that also impact the response to AraC, the key backbone to intensive chemotherapy protocols used in AML. Two targets were identified, TRMT5 and CTU2. This study focuses on TRMT5, a protein responsible for N1-methylguanosine (m1G) in both cytosolic and mitochondrial tRNAs at the guanosine in position 37. Employing nanopore sequencing technology, the authors were able to show that TRMT5 knockout specifically reduces m1G at position 37 of tRNA. The reduction on m1G could be rescued by expression of full length TRMT5, but not a catalytically-dead mutant. Importantly, deletion of the mitochondrial transfer sequence in TRMT5 abrogated its ability to rescue m1G levels in the mitochondrial tRNA pool. Consistent with this, mitochondrial protein synthesis was reduced by loss of TRMT5, however total mitochondrial mass was unchanged.

Considering that increased oxidative phosphorylation is appreciated as a cellular adaptation that can facilitate tolerance to chemotherapy, and that this metabolic switch requires an upregulation in mitochondrial protein synthesis, the authors investigated if changes in mitochondrial respiration contribute to the synthetic lethality of TRMT5 loss in the presence of AraC. Chemotherapy-persistence is defined as a temporary condition in which a population of AML cells can survive during chemotherapy treatment without overt genetic resistance. Here, the AraC-persistent cell lines exhibited the lowest oxygen consumption rates and the lowest electron transport chain gene expression compared to AraC-sensitive AML cell lines. Importantly, due to their capacity to increase mitochondrial protein synthesis, AraC-persistent cells were able to rapidly increased oxygen consumption upon exposure to chemotherapy, whereas the AraC-sensitive cell lines could not. This rapid increase in oxygen consumption in AraC-persistent cells was prevented by loss of TRMT5, which also restored chemotherapy sensitivity. The authors were able to identify patients with chemotherapy resistance through the low expression of mitochondrial electron transport chain genes, a finding that was confirmed in multiple independent data sets. This finding appeared to be independent of adverse genetic features, such as p53 loss of function, although a comprehensive multivariate analysis was not possible due to patient numbers. The authors also used an elegant inducible system in which TRMT5 could be degraded (the dTAG system), to demonstrate specificity and proof of principle that degrading TRMT5 synergized with the effects of chemotherapy and venetoclax, indicating that this approach may be relevant to low-intensity approaches in addition to restoring response to intensive chemotherapy.

This work extends our understanding of the complex and tightly regulated processes that govern RNA biology and conceptually provides proof of principle that modulating RNA modifications can be leveraged to develop new therapies for patients with blood cancers.

Specifically, targeting of TRMT5 was able to “second guess” the cancer cell’s response to chemotherapy, and by blocking these adaptive changes, could prevent chemotherapy resistance. More broadly, this work highlights the central importance of oxidative phosphorylation and mitochondrial function in response and resistance to chemotherapy and venetoclax combinations in AML, justifying the targeting of mitochondrial adaptation as a highly tractable and clinically-relevant approach to optimize the efficacy of current AML treatments.

There has been a revolution in the treatment of patients with AML, with access to targeted therapies, novel low-intensity combinations and the future promise of immunotherapy or even cellular therapy. Accordingly, in 2025, more patients have access to highly effective treatments resulting in better survival, when compared to any time in the past. Despite this, many subgroups of patients (eg, those with TP53 mutations or adverse risk genetics) continue to have a dismal prognosis, even with the best available therapy. Ultimately, to overcome these clinical challenges we will need to think outside the box, to decode new treatment paradigms. Novel approaches, such as targeting regulators of RNA modifications, may provide a new avenue to address these challenges.

Conflict-of-interest disclosure: M.B. has received research funding from Bristol Myers Squibb and Cylene Pharmaceuticals. S.W.L. has received research funding from Bristol Myers Squibb and has consulted for AbbVie, Novartis, Astellas, and GlaxoSmithKline.