An ancient RNA-guided system could simplify delivery of gene editing therapies

Amazing stuff!

"A vast search of natural diversity has led scientists ... to uncover ancient systems with the potential to expand the genome editing toolbox. These systems, which the researchers call TIGR (Tandem Interspaced Guide RNA) systems, use RNA to guide them to specific sites on DNA. TIGR systems can be reprogrammed to target any DNA sequence of interest, and they have distinct functional modules that can act on the targeted DNA. In addition to its modularity, TIGR is very compact compared to other RNA-guided systems, like CRISPR, which is a major advantage for delivering it in a therapeutic context.  ...

The TIGR-associated (Tas) proteins that Zhang’s team found share a characteristic RNA-binding component that interacts with an RNA guide that directs it to a specific site in the genome.

They note that CRISPR systems can only be directed to segments of DNA that are flanked by short motifs known as PAMs (protospacer adjacent motifs). TIGR Tas proteins, in contrast, have no such requirement. “This means theoretically that any site in the genome should be targetable,” ... The team’s experiments also show that TIGR systems have ...  a “dual-guide system,” interacting with both strands of the DNA double helix to home in on their target sequences, which should ensure they act only where they are directed by their RNA guide. What’s more, Tas proteins are compact—a quarter of the size Cas9 on average—making them easier to deliver, which could overcome a major obstacle to therapeutic deployment of gene editing tools.  "

From the abstract:

"RNA-guided systems provide remarkable versatility, enabling diverse biological functions. Through iterative structural and sequence homology-based mining starting with a guide RNA-interaction domain of Cas9, we identified a family of RNA-guided DNA-targeting proteins in phage and parasitic bacteria.

Each system consists of a Tandem Interspaced Guide RNA (TIGR) array and a TIGR-associated (Tas) protein containing a Nop domain, sometimes fused to HNH (TasH) or RuvC (TasR) nuclease domains.

We show that TIGR arrays are processed into 36-nt RNAs (tigRNAs) that direct sequence-specific DNA binding through a tandem-spacer targeting mechanism.

TasR can be reprogrammed for precise DNA cleavage, including in human cells. The structure of TasR reveals striking similarities to box C/D snoRNPs and IS110 RNA-guided transposases, providing insights into the evolution of diverse RNA-guided systems."

An ancient RNA-guided system could simplify delivery of gene editing therapies | Broad Institute "The programmable proteins are compact, modular, and can be directed to modify DNA in human cells."

An ancient RNA-guided system could simplify delivery of gene editing therapies "The programmable proteins are compact, modular, and can be directed to modify DNA in human cells."

TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses (no public access)

The Tas protein uses an RNA guide to recognize a specific target DNA sequence.

Mutations in two gene pairs point to a promising drug target in 5 percent of adult cancers

Good news! Cancer is history (soon)!

The article contains attention grabbing headings like "Lethal pairings" and "Superkiller complexes". Beats any suspense story! 😊

"Scientists ... have discovered that about 5 percent of adult cancers rely heavily on a gene called PELO to survive and that disabling the gene kills those cancer cells. These cancers have mutations in one of two genes, FOCAD or TTC37. ...

The team began by looking for ways to target a common set of cancers in which both copies of chromosome 9 have a deletion in a region called 9p21.3. These mutations occur in a range of deadly cancers including those of the brain, bladder, pancreas, esophagus, and lungs. ...

But the cells with 9p21.3 deletions were not the only ones with a PELO dependency. Another group of cells with high microsatellite instability — mutations in short repeated DNA sequences, specifically in the TTC37 gene — had the same sensitivity. That meant there are potentially two groups of patients who might benefit from drugs targeting PELO: those with deletions in FOCAD and others with deletions in TTC37, which are found in colorectal and endometrial tumors. ..."

From the abstract:

"Cancer genome alterations often lead to vulnerabilities that can be used to selectively target cancer cells. Various inhibitors of such synthetic lethal targets have been approved by the FDA or are in clinical trials, highlighting the potential of this approach.

Here we analysed large-scale CRISPR knockout screening data from the Cancer Dependency Map and identified a new synthetic lethal target, PELO, for two independent molecular subtypes of cancer: 

biallelic deletion of chromosomal region 9p21.3 or 

microsatellite instability-high (MSI-H).

In 9p21.3-deleted cancers, PELO dependency emerges from biallelic deletion of the 9p21.3 gene FOCAD, a stabilizer of the superkiller complex (SKIc).

In MSI-H cancers, PELO is required owing to MSI-H-associated mutations in TTC37 (also known as SKIC3), a critical component of the SKIc.

We show that both cancer subtypes converge to destabilize the SKIc, which extracts mRNA from stalled ribosomes.

In SKIc-deficient cells, PELO depletion induces the unfolded protein response, a stress response to accumulation of misfolded or unfolded nascent polypeptides. Together, our findings indicate PELO as a promising therapeutic target for a large patient population with cancers characterized as MSI-H with deleterious TTC37 mutations or with biallelic 9p21.3 deletions involving FOCAD."

Mutations in two gene pairs point to a promising drug target in 5 percent of adult cancers | Broad Institute "Targeting the PELO gene could be a way to kill tumor cells in cancers with one of two common genetic mutations."

Towards mapping the landscape of cancer vulnerabilities across all tumors "To accelerate precision cancer medicine, we construct systematic key datasets, analytical and visualization tools, using broad panels of cancer models that represent the diversity of human cancers."

SKI complex loss renders 9p21.3-deleted or MSI-H cancers dependent on PELO (open access)

Fig. 1: Analyses of DepMap data to identify dependencies associated with 9p21.3 deletion.