Synthetic lethality in cancer cells by programmable RNA editing 

PI:

Silvestro Conticello

Email:

silvestro.conticello@cnr.it

Affiliation:

Istituto di Fisiologia Clinica - CNR

ORCID:

0000-0002-4244-1846

Objective: Development of programmable RNA editing as a tool to interfere with specific cellular processes and trigger selective cell death in cancer by targeting cellular processes in a synthetically lethal relationship with processes already altered in the cancer cells.

Synthetic lethality is a condition where simultaneous occurrence of two specific alterations, not individually lethal, results in the death of a cell. This concept has been applied to cancer therapy by targeting gene products in a synthetically lethal relation with pathways already disrupted in the cancer cell. While this approach offers the potential to selectively target cancer cells while preserving healthy ones, its effectiveness has been hindered by the difficulty to identify and exploit patient-specific synthetically lethal gene pairs.

RNA editing is physiological process mediated by enzymes -the ADARs and the APOBECs- that deaminate respectively adenosines and cytidines into inosines and uracils. As inosines are read as guanosines by the translation machinery, editing can cause recoding of the transcript. These posttranscriptional modifications can affect expression, splicing, RNA structure and structure or function of the translated product.

In recent years programmable RNA editing is being developed as a potentially safer approach to genome editing. This is due to the transient nature of RNA editing, which avoids inducing permanent changes to genetic information. Several approaches have been developed, based on oligonucleotides that recruit either a deaminase (ADARs or APOBECs) or an engineered deaminase (e.g., dCas13-APOBEC3A or Cas7-11-ADAR2) to the target RNA.

Aim of the task is to use patient-specific cancer genome/transcriptome-based information to define exploitable targets whose temporary alteration by programable RNA editing specifically targets cancer cells while sparing healthy cells: the transient nature of RNA editing does not introduce alterations in the genetic information of the cell, thus posing lower risks on bystander cells compared to DNA-targeting technologies; moreover, RNA editing is a more versatile approach compared to a drug-based one, as it allows to recode and alter virtually every cellular transcript.

The project is structured in three phases:

  1. Selection of the most suitable technologies for programmable RNA editing.
  2. Selection of the exploitable targets to induce synthetic lethality in cellular and animal models.
  3. Validate the most appropriate RNA editing strategy for each target (induction of stop codon, alteration of splicing, etc.) by cellular assays (induction of cell death, effects on bystander cells), imaging (high-resolution microscopy, nanoscopy), and RNA/DNA sequencing.
 
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