December 13, 2023

Shedding light on 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 perhaps the most cellularly important of these “Dark Side” molecules called regulatory RNAs (regRNAs) that directly control the expression of nearby protein-coding genes. With our proprietary RAP Platform™, CAMP4 can identify and sequence the regRNA that controls the expression of any disease-associated gene, allowing us to develop antisense oligonucleotide therapies (ASOs) to modulate expression by targeting the regRNA, thereby treating genetic disease.

In this article, I’ll introduce CAMP4’s approach to identifying and targeting regRNAs using our platform, and describe how our regRNA-targeting therapies have the potential to 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 act locally, within their defined neighborhoods. While a gene may be controlled by multiple regRNAs, there is typically one having the greatest impact on RNA expression. We have developed a proprietary platform (RNA-actuating Platform, or “RAP”) to identify the most impactful regRNA for each gene.

A regRNA may be engaged to either 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. This allows us to displace negative-acting factors from the regRNA complex during active transcription and effectively remove the “brakes” on the process, amplifying RNA production from the disease-associated gene.

Boosting protein production in genetic diseases

CAMP4 is developing therapies for genetic diseases caused by gene mutations that result in inadequate protein production. In some diseases, a mutation in one allele results in under-expression of a gene and inadequate production of the needed protein – a class of disease referred to as haploinsufficient; for these diseases, we seek therapeutic mechanisms that increase expression of the healthy allele. In other diseases, our therapeutic approach seeks to augment production of an already healthy level of protein in order to compensate for a defective downstream biological process – an approach referred to as gene augmentation. In describing how we use our RAP Platform to discover targets and develop needed therapies, I’ll focus on our usage of the gene augmentation approach to address urea cycle disorders (UCDs).

UCDs are a group of diseases resulting from genetic defects in the urea cycle, which converts ammonia, a byproduct formed by the normal breakdown of amino acids in the body, into urea, which the body excretes in urine. This conversion occurs in a series of biochemical reactions, with each step catalyzed by a specific enzyme. A mutation in any of the genes encoded within the urea cycle will result in insufficient functional enzyme and impact the body’s ability to metabolize ammonia, resulting in toxic levels of ammonia building up in the blood and causing damage to the brain.

CAMP4’s UCD programs targets carbamoyl phosphate synthetase I (CPS1), which catalyzes the first step of the urea cycle. Although CPS1 mutations underlie a very small fraction of UCD cases, our program is actually intended to treat UCD caused by deficiencies in remaining urea cycle enzymes, downstream from CPS1. The therapy CAMP4 is developing releases the transcriptional “brake” on the CPS1 gene to increase its expression and thus boost the level of activity at this step. This boost results in greater flux (conversion of ammonia to urea) throughout the rest of the cycle – regardless of which downstream step has the specific genetic deficiency.

CAMP4’s program is intended to act as a pan-UCD therapy addressing the vast majority of UCD subtypes, and has the potential to become a backbone therapy upon which genetic subtype-specific treatments, such as therapeutic candidates for OTC-deficient patients, could be overlaid. We anticipate dosing healthy volunteers in a Phase 1 UCD study early next year.

Finding and releasing the genetic brakes

To identify “braking” regRNAs, we start with a proprietary AI-based model that elucidates the interactions occurring within the insulated neighborhood containing the disease-related gene and points us to the regRNA sequences that have the strongest effect on its expression. We then conduct additional experiments to identify the specific region within the regRNA that controls that gene.

Next, we design and optimize ASOs that target the regRNA sequence of interest. We use ASOs because they are a well-established therapeutic modality that act efficiently in the nucleus and use biology’s most fundamental rules for engaging RNA.

Our ASOs, which we refer to as RNA Actuators, increase levels of the gene expression by up to two-fold. In UCD, we believe this boost will be sufficient to increase the overall activity of the urea cycle and have a meaningful therapeutic effect. But, UCD is just one group of genetic diseases that CAMP4 has the potential to treat using its RAP Platform. There are hundreds of other genetic diseases in which increasing the relevant gene’s output, whether through a haploinsufficient or gene augmentation approach could mean the difference between sickness and health. We are at the forefront of this next frontier of the regulatory genome – and we’re just getting started.