LncRNAs, CRISPR, Cancer

CRISPR/Cas9 genome engineering tools to discover lncRNAs in cancer

Our challenge is to discover a small group of cancer-related lncRNAs amongst tens of thousands of potential candidates. The newly-discovered genome-engineering technology, CRISPR/Cas9, represents a uniquely powerful tool for achieving this. Not only can CRISPR/Cas9 be used to manipulate lncRNAs in their endogenous environment, it can also be used at high throughputs.

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Genomic deletion using DECKO: two Cas9 proteins (scissors) are targeted by single-guide RNAs (ribbons) to sites flanking the target region. (Photo: Didac Santesmasses)

Our lab recently developed a tool, called DECKO, which enables one to delete virtually any desired genomic region using pairs of CRISPR/Cas9 complexes. We use DECKO to study lncRNAs, either silencing them by deleting their promoter, or else by leaving expression intact and removing fragments of their exons. The power of DECKO is that it is highly scalable: we can use it equally to target a single lncRNA, or thousands of lncRNAs in parallel. This enables us to screen for new cancer lncRNAs.

DECKO creates the need for bioinformatic design of CRISPR/Cas9 targeting constructs. We have created a design pipeline for this, called CRISPETa.

We are presently using the DECKO and CRISPETa tool kit to discover new lncRNAs in various human cancers. The lncRNAs we find will give us new insights into the molecular pathways controlling oncogenesis, and hopefully provide new targets for therapy.

You can read more about these approaches here:
Aparicio-Prat et al, DECKO
Pulido-Quetglas et al, CRISPETa