Novel Approach To Cancer Explores Severing Its Genetic Supply Line

By Eric B. Kmiec, Ph.D., executive director of ChristianaCare’s Gene Editing Institute and chief scientific officer of Corrixr Therapeutics

While incredible innovations in cancer therapeutics have emerged over the last decade, most suffer from one of a few issues:

• they are non-specific to the cancer itself (chemotherapy, radiotherapy),
• they fail over time because the tumor develops resistance (systemic therapy, chemotherapy, radiotherapy, immunotherapy),
• they are incapable of adapting to changes within the tumor microenvironment (immunotherapy), and
• they require excessive priming or they are overly toxic (all of the above).

Therefore, if you are not fortunate enough to cure cancer when it's early with surgery or other treatments, eventually the tumor spreads and patients experience greater suffering and a greater possibility of death.

Precise and efficient gene editing/gene ablation represents one of the most important and genuinely novel approaches to treating cancer. Gene ablation's very targeted approach is the type of cancer treatment that just might address the challenges listed above and is frankly the definition of "precision medicine." Not only can we attack cancer at its very source, but we can also adapt and evolve with cancer in real time, disrupting how the tumor cells survive, particularly when under attack from more standard anti-cancer treatments.

While the concept of using a genetic tool to treat disease has held a certain fascination for molecular geneticists like me for many years, it was the discovery and democratization of CRISPR that convinced me that we could transition gene editing from bench to bedside.

It is true that other tools already existed, including zinc finger nucleases (ZFNs) and TALENs, but none of these tools have the scalability or ease of manufacturing that CRISPR provides. CRISPR/Cas9 is a pathway of enzymatic activities, resident in most bacterial cells, that functions to fight off viral infections, much like the human body uses antibodies. Bacterial cells are under constant attack from bacteriophages, and CRISPR systems chop and degrade the invading viral DNA to prevent infection, a sort of bacterial innate immunity. Some scientists have re-engineered and repurposed CRISPR, away from how it naturally functions, to change individual DNA bases in a process known as base or prime editing. And there have been a few success stories, as evidenced by the Baby KJ case at Children's Hospital of Philadelphia and the University of Pennsylvania. Like many of our colleagues around the world, we were delighted upon hearing the news that base editing had been used successfully on a child to reverse the devastating effects of severe carbamoyl-phosphate synthetase 1 deficiency (CPS-1 deficiency). This unique N = 1 case gives hope to those who suffer from rare diseases where traditional drug treatments have failed. This work followed the pioneering efforts of companies like Intellia and Vertex in the development of CRISPR drugs to treat other genetic diseases such as transthyretin amyloidosis TTR and sickle cell disease.

Attacking A Pathway That Enables Tumor Cell Survival

So, how do we use CRISPR for the treatment of cancer where the villain is not a malfunctioning metabolic error but rather the uncontrolled growth of healthy cells that have been transitioned to the oncogenic state? Certainly, one could envision using base or prime editing to reverse driver mutations in tumor suppressor genes. An intriguing thought, no doubt, but the molecular mechanism of oncogenesis incorporates a mutator phenotype where enhanced replication of tumor cells creates a fertile ground for continuous genetic change. Hence, reversing single base mutation(s) would only suppress those altered tumor cells temporarily because the mutagenic heterogeneity within the population will circumvent correction of any previous mutations. It’s akin to the adage, "we’d simply be chasing our tails."

Instead, we chose to focus on disrupting or chopping up genes, like the master regulator NRF2, because it acts as a survival control center for the growth of many squamous cell cancers. It has largely been undruggable by traditional small molecules or antibodies, blocked by its dynamic protein structure, its biological control, and the limits of conventional pharmacology. We believe that CRISPR can disable (chop) the NRF2 gene efficiently enough to permanently disable the protein supply chain, creating an environment in which tumors that rely heavily on NRF2 for energy production and metabolism would die when the genetic supply line is severed.

During our early days, we paused and asked: "What we are actually targeting?" And we realized that the tumor itself is not the problem. The limits of our pharmacology are. Oncology drug development has historically focused on targeting oncogenes (with driver mutations) and cell surface markers that reflect the biology of how cancer starts and presents, not how it survives.

Yet clinical outcomes are largely determined by the tumor’s ability to survive, after or in response to treatment, not how the tumor originated.

When a cancer cell transitions, it is true that most often an oncogene has driven the transformation. But once it is transformed, the tumor can survive independently of how it got there, particularly if it rewires its metabolism to create a novel metabolic engine that meets its ever-growing demand for energy. This also helps with dealing with stress, such as the response to cancer treatment and its capacity for rapid growth, which often deprives and exhausts its energy-generating systems.

As mentioned above, a major regulator of tumor cell survival is NRF2, a transcription factor controlling 200 genes in pathways that collectively constitute a major part of the tumor survival infrastructure.

These include:

• redox detox, which neutralizes chemo and radiation;
• generated reactive oxygen species via glutathione;
• metabolic rewiring, which redirects the cell to use alternative pathways for energy generation;
• immune-evasion, which expresses STING mediated interferon signaling and reduces MHC-1 surface presentation, which blocks the immune recognition that almost all IO therapies depend on; and
• a collection of well-known oncogenic activities, including apoptosis suppression, anoikis, invasion, and metastasis.

Remarkably, NRF2 drives nine out of 11 hallmarks of cancer simultaneously, acting as a scaffolding around which the tumor reorganizes its biology once the squamous cell tumor constitutively activates NRF2. In the addictive state, many tumor cells cannot function without NRF2. In other words, whereas normal cells tolerate NRF2 loss, NRF2-addicted tumor cells do not.

Adding CRISPR To The Anti-Cancer Armament

Almost every current major treatment approach is extracellular, targeting surface proteins, oncogenes, and the structural markers on the outside of the cell. For example, chemotherapy and radiation are nonspecific; they kill broadly and require toxicity levels most patients cannot sustain or tolerate. Immunotherapy is effective in approximately 30% of most cancer populations, so in essence it fails most patients. Cell therapy relies on receptors on the cell’s surface that identify a tumor cell, and the number of receptors on the tumor cell randomly determines whether the tumor cell will be efficiently killed.

It’s a game of chance. But in all cases, no matter what the therapy is, the tumor’s genetic target mutates away, and the tumor survives untargeted and targeted therapies. The result of all of this is approximately 90% of solid tumors ultimately fail treatment. Patients cycle through multiple lines of therapy, each providing temporary benefit before failure. What has not been done is to address how the tumor cell survives, its internal metabolic engine, not how it looks from the outside.

Corrixr Therapeutics' CRISPR drug, CXR-101, does more than carry out genetic ablation of the NRF2 gene; it's designed to collapse the tumor's survival capacity. Normal cells tolerate NRF2 loss because they never reorganize their survival infrastructure around it, and normal metabolic processes can support growth. NRF2-reliant or -addicted tumors are different. They've let their backup systems atrophy and rewired core metabolic processes around NRF2 as their single load-bearing support.

The NRF2 inhibitor landscape reveals a series of important small molecules targeting NRF2. Many of these rely on elevated levels of NRF2 caused by mutations in exon 2 to either the NRF2 gene or, more frequently, the KEAP1 gene. These small molecules struggle for sustainable efficacy because NRF2 routinely undergoes a form of genetic rearrangement known as exon skipping.

The scientists at the Gene Editing Institute/Corrixr were among the first to report on exon skipping in NRF2. This genetic alteration shifts the encoded domains in the protein and explains why different versions of the NRF2 protein become completely immune to small molecules because the target site within NRF2 no longer exists.

Epigenetic variations of NRF2 are also known to be prevalent. In a tumor, the NRF2 protein target is actually a diverse population of NRF2 proteins with various, sometimes modified, functional domains that can make it challenging for an inhibitor to bind to enough protein in the long term to exhibit sustained anti-cancer effects. This requirement is played out in mouse models, where heavy, almost unreasonable levels of drug need to be introduced into the mouse on a daily basis.

In contrast, CXR-101 acts on a fixed genetic target whose number does not change since NRF2 genes are not amplified, even during oncogenesis. CXR-101 is agnostic to the tumor profile since it targets a site within the gene that does not mutate or evolve in over 30 types of squamous cell carcinomas. CXR-101 is also mutation agnostic, a fixed, genetically stable target. The level of NRF2 in a tumor cell varies widely and therefore the dosing is unpredictable using small molecules. As mentioned above, the genetic copy of the gene is fixed, and so, per cell, there are two or three targets for CRISPR to destroy. That is why a small number of edited cells can make a difference. Genomic DNA is always present and accessible for CRISPR targeting, whereas NRF2 protein expression is reactive to the state of the cell. NRF2 is active in the nucleus, where it does all its work; small molecules for NRF2 are limited to cytoplasmic degradation. NRF2 also has a very short half-life within the cell, making it potentially more challenging to inhibit.

Finally, CXR-101 is not salvage therapy. It is not something a patient receives after chemotherapy, radiation, or immunotherapy fails; rather, it addresses a survival mechanism that all these therapies are fighting against anyway. We hope it will be the first genetic intervention for any patient with an accessible squamous cell carcinoma.

About The Author:

Eric B. Kmiec is founder and chief scientific officer at Corrixr Therapeutics, a genetic medicine company targeting squamous cell cancers. He's also the executive director and chief scientific officer at the Gene Editing Institute, part of the Christiana Care Health System based in Delaware. He received his Ph.D. in molecular biology and biochemistry from the University of Florida.