MicroRNAs and non-coding RNAs in development and disease

The recent discovery of thousands of non-coding RNAs (ncRNAs) with regulatory function is redefining the landscape of transcriptome regulation, highlighting the interplay of epigenetic, transcriptional and post-transcriptional mechanisms in the specification of cell fate and in the regulation of developmental processes. We have witnessed to the identification of an increasing number of either small regulatory RNAs (such as microRNAs, miRNAs) or long non-coding RNAs (lncRNAs) with a critical role in the regulation of molecular circuits associated to numerous biological processes. Essentially all known physiological and pathological processes, including cancer, are regulated by miRNAs and lncRNAs, which can work together to mark differentiation states or alone as authentic oncogenes or tumor suppressors.

1. Dynamics of miRNA regulation in physiology and cancer

Overall, the levels of miRNAs in cells are determined by the sum of two processes: biosynthesis, which generates new miRNA molecules, and decay, which clears old miRNAs. So far, the decay of miRNAs has not been properly elucidated in cancer, due to the lack of proper methodologies. We recently developed new tailored approaches based on in vivo RNA labeling and high-throughput sequencing to study the modes and the mechanisms of miRNA decay ( Marzi, Ghini et al., Genome Res 2016). This has allowed us to precisely measure miRNA biosynthesis and decay rates in cells, and has revealed the existence of different pools of miRNAs, distinguished by their decay patterns. Hence, miRNAs are not just stable molecules as previously thought. However, the investigation of such mechanism in cancer is still missing. We propose to apply our approaches to models of human cancer to investigate i) the role of decay in the regulation of miRNAScreen%20Shot%202017 01 23%20at%2015.48.12s in cancer and ii) the critical mechanistic steps associated with this process.

We are interested in characterizing the activity of either miRNAs or lncRNAs, as part of complex circuits that control cell fate and differentiation, integrated with signaling networks and the transcriptional framework ( Tordonato et al., Frontiers Genetics 2015).

We hav
e developed multiple approaches to search for non-coding RNAs able to act as “markers” of stem-cells (SCs) or “modifiers” of stem cell functions, including i) the isolation of RNAs specifically expressed in SCs; ii) unbiased genetic screens to search for non-coding RNAs able to regulate stem cell properties; and iii) mutant mice, to deconvolute the role of endogenous molecules in the regulation of tissue homeostasis and cell. In collaboration with other groups at IIT, we are also exploiting different synthetic platforms (i.e. nanoparticles) as carriers for delivering RNA-based therapeutics into cancer cells. We intend to follow up these studies to

  1. highlight the miRNA- and lncRNA- based circuitries that control the identity and the plasticity of epithelial cells
  2. pinpoint the role of specific RNA molecules as potential therapeutic agents for the treatment of even the most aggressive forms of cancer.

Computational Tools:

isomiRage: a desktop application that counts the number of occurrences of miRNA isoforms from NGS data (in a Bowtie .map alignment file)

Collaborations

  • D. De Petri Tonelli ( NBT@IIT Genova) –  RNA profiling in differentiating neural stem cells (NSCs)
  • S. Giordani ( D3@IIT Genova) –   Nano-carbon materials for RNA delivery
  • PP. Pompa ( D3@IIT Genova) –  Nanomaterials for miRNA delivery and detection
  • PP. Di Fiore (IFOM-Milan, IEO-Milan) – miRNAs in breast cancer stem cells
  • Y. Torrente (UniMi – Milan) – Non-coding RNAs in human mesenchymal stem cells (MSCs)
  • M. Mapelli (IEO-Milan) – Molecular basis of asymmetric cell division