isomiRGate: a comprehensive gateway for studying the canonical and modified microRNAomes in Cancer

PROJECT SUMMARY According to the statistics provided by the American Cancer Society, in 2023, about 1.9 million new cancer cases will be diagnosed in the United States, and more than 609K people will die from this disease. Such data firmly highlights the importance of continued efforts to find new and effective ways to detect and treat cancer, with the

ultimate goal of reducing the number of diagnoses and fatalities. Epitranscriptomics has lately enlarged insights into the field of cancer biology. RNA modifications occur in coding and non-coding RNAs (ncRNAs), including microRNAs (miRs). miRs are small single-stranded ncRNAs, which play a crucial role as negative regulators of

gene expression, typically via partial base-pairing complementarity with their target transcripts. Post- transcriptional modification phenomena associated with miRs, such as imprecise cleavage of the miRNA sequence and Adenosine-to-Inosine RNA Editing events, can alter the miR canonical sequence and function.

Recently, modified miRs (miR isoforms) have been proposed as potential innovative biomarkers for cancer diagnosis and surveillance. However, concurrent profiling of modified miRs has yet to be investigated in cancer properly. Additionally, no online resource offers easy and comprehensive consultation to study miR isoforms in

cancer. Solutions to these gaps would positively impact discovering novel potential cancer biomarkers and uncovering cancer-related mechanisms associated with a broader miRNAome. Recently, we concurrently profiled canonical and modified (e.g., shifted or DNA/RNA edited) miRs in >13K adult and pediatric cancer

samples from The Cancer Genome Atlas (TCGA) and The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) repositories (38 cohorts) (Distefano et al. 2022, Cancer Research). We accurately identified >8K expressed miR isoforms (>5-fold the canonical miRs). By merging canonical and

modified miRs, we boosted the quality of clustering results by improving the patients’ clinicopathologic stratification. Additionally, the broader miRNAome profiling uncovered a larger number of significant prognostic signatures. We also implemented an ad-hoc miR isoform-target prediction method and validated unique targeting

for a shifted miR isoform. Therefore, our proposal intends to outline (1) the function and (2) the post- transcriptional regulation of the broader miRNAome in a cancer-context manner by in-silico analyses and experimental validations. Moreover, to make the extensive amount of generated data available to the scientific

community, we propose (3) building isomiRGate, a freely accessible online gateway. isomiRGate platform will serve as a tool to I) elucidate the role of miR isoforms as potential cancer biomarkers and II) deduce the function and regulation of the broader miRNAome in cancer. We aim to create a platform, isomiRGate, adaptable to new

analysis methods, holding the potential to lead to the discovery of novel therapeutic targets for treating this deadly disease, with anticipated future clinical applications.