6. CONCLUSION
Rapidly accumulating evidences of the role of RNA modifications in cell
differentiation and development and their dysregulation in cancer have
emerged in the last years (Barbieri and Kouzarides, 2020;
Rosselló-Tortella et al., 2020). Although still in its infancy, the
potential of pharmacological targeting of RNA modifiers for reverting
aberrant epitranscriptomes strongly energized the research of chemical
biology and drug discovery in this field (Boriack-Sjodin et al., 2018).
Below, we highlight some of the key limitations and challenges that will
need to be addressed in the near future to improve the drug discovery in
the RNA scenario (Figure 2 ).
It should be noticed that the field does not start from the zero
\soutpoint, since the structures of key enzymes (writers, erasers) and
reader proteins are currently well-characterized. This is a good
starting point for guided and precise design of small compounds
targeting these structures based on computational methods. To date a
sizeable number of epitranscriptomic inhibitors have been reported, but
in actuality not all small molecule inhibitors have demonstrated
acceptable target potency or enzyme selectivity. Thus, there is an unmet
need to develop selective and more effective small-molecule inhibitors
of RNA modifiers for therapeutic applications. Apart from rational
chemical design approaches, we still need to learn more about the
biochemistry of RNA modifiers, their ligand binding pockets and the
downstream pathways.
A very important matter to consider is our current limited vision of the
mode of action of RNA modifiers. In other words, we are establishing
associations between two observations (i.e., an altered m6A level and a
tumour-suppressive effect) but, to date, we cannot determine causality
between both observations. Most of the studies trying to establish
phenotypic connections applied approaches that involve genetic
manipulation of the full RNA-related gene. These approaches do not allow
to solve whether the resulting phenotype is due to “druggable”
biochemical mechanisms (e.g., enzyme catalysis or ligand binding) or
other non-easy actionable targets linked to protein interactions (e.g.,
scaffolding, protein–protein interactions or chaperone mechanisms)
(Boriack-Sjodin et al., 2018). Or even less, whether the RNA
modifications result in changes in secondary structures or
protein-protein interactions is still uncertain.
More sophisticated biological approaches apart from cell-based assays
are essential to identify the functional effects of targeting the
epitranscriptome. On the basis of what we have learned from epigenetic-
based therapy, it is expected that RNA modifications work in multimeric
protein complexes. Consequently, the translation of the results obtained
in in vitro cell based assays do not replicate the physiological
conditions from in vivo models. Animal models carrying RNA
modification defects (e.g., inducible knockout or mutant mice for
RNA-modifying enzymes) are a move in the right direction to unravel the
physiological function of RNA modifications. Furthermore, as previously
described (Cheng et al., 2018; Huang et al., 2019a), most of the actual
RNA modifying enzymes shared catalytic sites and cofactors with DNA and
histone epigenetic machinery, and thus, drug-based intervention on RNA
modifications can induce unforeseen effects on other regulation systems
including epigenetics.
Although we are seeing improvements, the high number of possible RNA
modifications and the complexity of molecular pathways involved are
still an impediment to evaluate the biological consequences of small
molecules intervention targeting the epitranscriptome (Jia et al., 2011;
Wang et al., 2014). An aspect of intense debate is whether the
ubiquitous nature of RNA modifications could increase the toxicity of
associated drugs as it would be extremely difficult to prevent a
pleiotropic effect. This knowledge, undoubtedly, also draws from the
technical side. RNA modification detection methods have shown a
tremendous improvement, particularly since the development of valid
methods for studying the epitranscriptome at wide scale using NGS
(Linder et al., 2015). Improvements to avoid methods dependent on
antibody recognition or site-specific cleavage linked to radiolabelling,
like MAZTER-seq (Garcia-Campos et al., 2019) or m6A-REF-seq (Zhang et
al., 2019), held promises to allow a better quantification and precision
of the epitranscriptome in specific contexts. Technological advances for
the identification and quantification of low-abundance RNA
modifications, establishment of internal standards as controls or
development of bioinformatic tools to generate, analyse, and standardize
protocols should be also a priority to ensure the reliability of the
data (Morena et al., 2018).
In overcoming these (and other) chemical, biological and technical
barriers, we will have a better and clearer view of the epitranscriptome
map, its contribution to signalling pathways and its role in human
health and disease. With this comprehensive overview of
“epitranscriptome Science”, the development of innovative therapeutic
intervention of RNA modifications will be an exciting reality.