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Tumor Discovery RNA-protein complexes deregulated in cancer

challenges, resulting in limited data on RNA structure single NOTCH2 and MAP1B mRNA transcripts in living
within BCs. A key obstacle is isolating this specific RNA cells, identifying mechanisms such as cotranslational
quantitatively. A recently reported needle-shearing translocation of NOTCH2 mRNA at the ER and MAP1B
method has proven effective for RNA extraction in this mRNA transfer to the cell periphery. These technologies
context. RNA structural biology is crucial for advancing provide insights into mRNA mislocalization and BC
knowledge, with cryo-EM SPA revealing protein-free dysregulation in diseases and cancer. New frontiers on
15
RNA structures. RNA structure determination using treatment of cancers by targeting RNA modifications and
cryo-EM methods provides useful information, including BC dysregulation with new drugs are surging interest and
resolving maps of RNA-based systems. These data can could be applied in a clinical setting. 298
offer subnanometer resolution and coordinate estimation,
especially when combined with multidimensional 6. Conclusion
chemical mapping and computational modeling, such as In conclusion, this review highlights the frontier of
with Rosetta DRRAFTER. The “Ribosolve” pipeline aids condensate- and oncogenic RNA-targeted drug discovery,
in validating macromolecular complexes. Applying this pointing to potential breakthroughs in therapeutic
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workflow to ncRNA modules may uncover new structural interventions. The role of BCs, including SGs, cancer-
elements. associated proteins, and tumor suppressors and repressors,
Super-resolution microscopy, based on various in cancer cell biology and their dysregulation within the
techniques, produces images with a resolution surpassing cancer milieu has gained attention. Several avenues exist
the diffraction limit, achieving the 30-nm range. A series for developing cancer therapeutics. The first involves
of fluorophores, acting in complementary absorbance targeting oncogenic ncRNAs, potentially delivering drugs
zones and emitting light at separate times and wavelengths, to specific cell types to prevent their role in forming phase-
enables resolving images over time. Among these methods separated condensates with oncogenic potential. This can
are super-resolution optical fluctuation imaging and be achieved through RNA silencing through shRNA or
single-molecule localization methods (SMLM). Examples ASO or by targeting triple helix structures. The second
of applications include imaging cell nuclei and mitotic approach focuses on targeting domains responsible for
stages. Stimulated emission depletion microscopy (STED), RNA–protein interactions. A third strategy is the use of
a frontline method in recent years, uses two laser pulses: drugs aimed at epigenetic enzymes. The final approach
an excitation pulse to excite fluorophores and a STED involves validating compounds that chemically disrupt
pulse for de-excitation through stimulated emission. BC formation or target the protein organizers of BCs.
Spectral precision distance microscopy resolves multiple Future research directions in BCs hold significant
light sources by isolating a few at a time. Cryogenic optical promise, offering not only a deeper understanding of
localization in 3D (COLD) localizes fluorescent sites within degenerative diseases and cancer but also paving the way
small- to medium-sized biomolecules at near-Angstrom for advancements in clinical applications.
resolution. Binding-activated localization microscopy
is a potential approach for SMLM. Stochastic optical Acknowledgments
reconstruction microscopy, another frontline method, is None.
similar to photo-activated localization microscopy (PALM)
and fluorescence photo-activation localization microscopy, Funding
which exploit sequential activation and time-resolved None.
localization of photoswitchable fluorophores to produce
high-resolution images. PALM of mEos3.2 fluorescent Conflict of interest
protein tags combined with DNA-PAINT revealed BC The authors declare that they have no competing interests.
organization and patterns in a cell cycle–dependent
manner. Spectrally resolved SMLM (SR-SMLM) combined Author contributions
with an environment-sensitive dye for displacement/
diffusivity mapping (SMdM) analyzed distinct Conceptualization: Palmiro Poltronieri
hydrophobic nanodomains at the condensate surface. 293-296 Visualization: Sudipta Joardar
290
Xia, Doudna, and colleagues developed single-molecule Writing – original draft: Sudipta Joardar
live-cell fluorescence in situ hybridization (smLiveFISH), Writing – review & editing: Palmiro Poltronieri
employing a programmable RNA-guided CRISPR–Csm Ethics approval and consent to participate
complex with catalytically inactivated Csm for specific and
durable RNA binding. Using smLiveFISH, they visualized Not applicable.
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Volume 3 Issue 4 (2024) 25 doi: 10.36922/td.4657