July 7, 2022

Finding light in the dark side of the genome: CAMP4’s approach to targeting regRNA in genetic diseases

The “Dark Side of the Genome” refers to the 98% of our genome that does not encode proteins. Once considered “junk” DNA that had no purpose or function, this “Dark Side” is now known to regulate the remaining 2% of our genome that codes for proteins.

CAMP4 is targeting a category of these “Dark Side” molecules called regulatory RNA (regRNA) that fine-tune the expression of nearby protein-coding genes. With our proprietary RAPTM Platform, CAMP4 identifies regRNAs that regulate the expression of disease-modulating genes, then develops antisense oligonucleotide (ASOs) therapies that target those regRNAs to treat genetic diseases.

In this article, I’ll introduce CAMP4’s approach to identifying and targeting regRNAs with our platform, and describe how our regRNA-targeting therapies treat genetic diseases.

What’s happening in the neighborhood

regRNAs are produced from DNA sequences found in the same chromosomal loop as the genes they control. These loops, called insulated neighborhoods, are a feature of the complex, three-dimensional structure of DNA, and thousands of them occur throughout the human genome. regRNAs tend to act locally, within their defined neighborhoods. While a gene can be controlled by multiple regRNAs, usually one has the greatest impact on RNA expression. We have developed a proprietary platform (EPICTM) to identify the most impactful regRNA for each gene.

Depending on its sequence, a regRNA may increase or decrease expression of its target gene. CAMP4’s initial focus is to target specific sites on a regRNA that will increase gene expression. The idea is to remove the regRNA “brakes” on a disease-modulating gene and allow it to produce more than its usual share of protein.

Boosting protein production in genetic diseases

CAMP4 is developing therapies for genetic diseases caused by gene mutations that result in inadequate protein, either because cells have only one healthy copy or they code for partially functional mutant protein. In describing how we use our RAPTM Platform to discover targets and develop our therapies, I’ll focus on our program for ornithine transcarbamylase (OTC) deficiency, where cells do not make enough functional protein.

OTC deficiency is caused by mutations in the OTC gene that produce a dysfunctional form of the OTC protein, which catalyzes a key step in the urea cycle. This cycle converts ammonia, a byproduct formed by the normal breakdown of amino acids in the body, into urea that the body excretes in urine. In the absence of a sufficient level of functional OTC protein, ammonia can build up to toxic levels in the blood and cause damage to the brain.

OTC deficiency is inherited in an X-linked recessive manner. This means that males only have one copy of the OTC gene; if that copy is mutated, they develop the disease. Females have two copies of the gene; if one copy is mutated, or if both are mutated, they will develop the disease. Depending on the specific OTC mutation or mutations the patient has, the resulting protein may be completely non-functional; or, as is the case for the majority of patients, it may still be partially functional.

For these patients, boosting production of the mutant protein – along with any fully functional protein that may be present – can be sufficient to treat the disease. The therapy CAMP4 is developing for OTC deficiency achieves this boost by releasing an regRNA “brake” on the OTC gene.

Finding and releasing the genetic brakes

To identify “braking” regRNAs, we start with a proprietary AI-based model that maps the interactions occurring in the insulated neighborhood of the disease-related gene and points us to the DNA sequences that have the strongest effect on its expression. Then, we conduct experiments to identify the specific regRNA that puts the brakes on that gene.

Next, we design, screen and optimize ASOs that target the regRNA. We use ASOs because they are a well-established therapeutic modality for interfering with RNA activity and can act efficiently in the nucleus.

Our ASOs, dubbed RNA Actuators, increase levels of the gene expression by up to two- to threefold. In OTC deficiency, this will boost the overall activity of OTC protein enough to have a therapeutic effect and decrease disease severity. There are many other diseases where increasing the output of normal protein function could have a meaningful therapeutic effect.

Interestingly, the most impactful regRNA identified for our OTC deficiency program from our AI-based model was also identified by another group studying OTC deficiency in human patients. These researchers identified a handful of patients having a mutation in the same regRNA, thus providing independent genetic validation of our therapeutic target.

OTC deficiency is just one genetic disease that CAMP4 has the potential to treat using its RAPTM Platform. There are literally thousands of other genetic diseases in which increasing the relevant gene’s output can mean the difference between a patient being sick and being relatively healthy. We are at the forefront of this next frontier of the regulatory genome – and we’re just getting started.