Genome Editing Tools and Techniques for Cancer Therapies

Ryan Leahy
3 January 2023
Cell Therapy
Clinical Trials
Gene Editing
Gene Therapy
Stem Cells
For this interview, Phacilitate’s Ryan Leahy speaks with Steve Kanner, PhD, CSO Caribou Biosciences, about the tools and techniques Caribou is utilizing in their gene edited CAR-T cell and iPCS-derived CAR NK cell programs, ahead of chairing the session ‘CAR-T Therapies: 10 Years On and the Future of CAR-T’ at Advanced Therapies Week 2023.
Can you please introduce yourself and describe your role within the Advanced Therapies Industry?

I am Steve Kanner the Chief Scientific Officer at Caribou Biosciences. I’m responsible for all of our therapeutic discovery and development, including all non-clinical R&D.

Caribou is currently working on a variety of different therapeutics. We are, in our heart, a CRISPR genome-editing biopharmaceutical company, and we implement next-generation CRISPR genome editing technology to generate allogenic cell therapies for cancer.

Can you describe what Caribou is currently working on?

The platform that we use is called chRDNA (pronounced ‘chardonnay’), which stands for CRISPR hybrid RNA/DNA. The reason that we use guides that contain both RNA and DNA in the backbone, compared to the natural form in which they are all only RNA, is that we observe very exquisite genome editing. We get very high efficiency on-target genome editing without the unintended off-target editing. What that means is that when we make a single edit, the risk of translocations occurring is dramatically because there aren’t multiple breaks in the chromosome.

In our product candidates, we perform multiplex editing where we intend to make multiple genome edits. Even though we have exquisite specificity, we do also have methods that enable us to reduce the likelihood of chromosomal rearrangements aswell. We combine these technologies to generate a variety of different therapies. Taking healthy donor-derived T cells, we implement the technology to eliminate the expression of the T cell receptor. Then at the site where we knock out the T cell receptor, we insert the CAR. So, we know exactly the specific chromosomal site where it’s inserted. In addition to that, we perform different edits to improve the persistence of these product candidates, because we know they’re allogeneic and will be rejected by the host quite rapidly.

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There are a couple of different strategies that we use to address persistence of antitumor response. One is to increase the amplitude of anti-tumor activity by knocking out a T cell checkpoint. Expression of the checkpoint receptor can otherwise lead to exhaustion of the CAR-T cells, so we eliminate that possibility. Another strategy is to enhance the time of the CAR-T cells in circulation. Here we play a little trick in which we knock out class I antigens by removing the stabvilixing protein (B2M) to precent patient T cell rejection of the CAR-T cells, and then insert one of the HAL antigens back into the CAR-T cells to prevent the patient’s natural killer (NK) cells from rejecting them.

The first approach was implemented in our first product candidate, CB-010, which now in the clinic being evaluated in non-Hodgkin lymphoma. The CAR target is CD19 and the additional edit to improve persistence is a knockout of PD-1. That’s important in those patients because the ligand for PD-1 (PD-L1) helps to prevent patient T cell destruction of the tumor, so we knock out PD-1 to enhance the anti-tumour activity of the CAR-T cells. The first cohort of data from the ANTLER Phase I trial was presented recently, and it showed that 100% of the 6 patients that were evaluated at the first dose level had complete responses, which is very exciting to see. We are currently escalating to higher dose levels and all data will be presented as it matures.

The second product candidate, CB-011, utilizes another persistence approach. It targets BCMA and is in development for multiple myeloma. We hope that we can retain the cells in circulation longer than they otherwise would be to help promote anti-tumor activity.

The third program is called CB-012 and it targets CLL-1 for acute myeloid leukemia. We haven’t, y divulged the different strategies that we’ll use to improve its persistence.

There is one more platform that we have built which uses induced pluripotent stem cells, or, iPSCs, that we differentiate into NK cells. We employ our genome editing technology to generate a multitude of edits for targeting solid tumors, then identify a clonal iPSC for generating the product candidate. The host of different armoring strategies that may be required for the challenge of targeting solid tumors is likely more vast than for targeting liquid tumors. Consequently, we’re thinking about a variety of different strategies there. We’re going to differentiate those iPSC cells into our NK cells because these immune cells have been shown to exhibit high anti-tumor and anti-metastatic activity, as well as improved safety profiles versus other immune cell based therapies.  


What are you currently most excited about in the cell and gene therapy space?

Over the last ten years, it’s been really exciting to see the emergence of tools for genome-editing being implemented in cell therapies. As an example, there’s the use of hematopoietic stem cells to drive the improvement of various diseases, like beta-thalassemia and sickle cell disease. People are now using genome editing to improve the integrity and veracity of these cells to help patients with these types of blood disorders. 

Also thrilling is, the implementation, of cell therapies as cancer treatments. There are several challenges in targeting cancers with cell therapies, but I think that path has been opened up by the development of autologous CAR-T cell programs. We’re excited that we can begin to address the challenges that many patients experience when trying to use their own cells and create a more universal approach.

The implementation of these genome editing techniques and tools for gene therapy, mean you will be able to directly target different tissues, to address a variety of different diseases where there are mutations that need to be corrected, such as cardio-metabolic diseases and inborn errors of metabolism. There are many different arenas where these various tools are going to be implemented to change the armamentarium of therapies that are available.

 What are you looking forward to about speaking at, and attending, Advanced Therapies Week 2023?

I’d say there are a few things I am excited about. One is the opportunity to hear about new technologies and new advancements in the field. The second thing is to make new connections with individuals in the industry who maybe I haven’t met thus far. And thirdly, to have an opportunity to be involved and lead a panel discussion that I hope will be interesting and informative for the attendees at the meeting!

Don’t miss Steve’s session, ‘CAR-T Therapies: 10 Years On and the Future of CAR-T’, on Thursday January, 19th 2023.

Join us at Advanced Therapies Week >>