Key Takeaways:
- A complete, ongoing response was seen in a hard-to-treat patient: In a first-in-human phase 1 trial, one patient with checkpoint-refractory metastatic colorectal cancer had a complete and ongoing response to gene-edited TIL therapy, sustained beyond 28 months.
- Knocking out CISH lowers the T-cell activation threshold: Editing tumor-infiltrating lymphocytes to remove the intracellular checkpoint CISH made them easier to activate, which is the rationale the trial set out to test.
- Immune repertoire sequencing traced the therapy at the clonal level: Deep T-cell receptor sequencing let the team follow individual infused T-cell clones in the patient’s blood for a year and connect immune-repertoire features to the clinical response.
- Early-phase safety and manufacturing held up: Across 12 dosed patients, the side effects traced to lymphodepletion and interleukin-2 rather than the edited cells, and a cell product was manufactured for 17 of the 19 patients in whom it was attempted.
Can Cell Therapy Reach Colorectal Tumors That Resist Checkpoint Drugs?
Most patients with metastatic colorectal cancer do not respond to immune checkpoint inhibitors, and treatment options thin out once standard chemotherapy and checkpoint drugs stop working. Cell therapy takes a different route. It gives the patient a large, targeted dose of their own tumor-reactive T cells.
In a recent webinar hosted by iRepertoire, a pioneer of the immune repertoire sequencing technology at the center of this story, Dr. Matthew Johnson presented results from a phase 1 clinical trial of gene-edited tumor-infiltrating lymphocyte (TIL) therapy in colorectal cancer. Dr. Johnson is a research scientist in Dr. Branden Moriarity’s lab at the University of Minnesota. The trial was published in The Lancet Oncology.
What Is CISH, and Why Knock It Out?
CISH stands for cytokine-inducible SH2-containing protein, a member of the suppressor of cytokine signaling family. In T cells, it works as an intracellular checkpoint. Under normal conditions, CISH binds PLC-gamma and promotes its degradation, which turns down T-cell receptor (TCR) signaling.
Remove CISH, and that brake comes off. PLC-gamma is no longer degraded, TCR signaling rises, and the activation threshold of the T cell drops. Less stimulation is needed to switch the cell on.
That is the therapeutic idea behind the trial. Editing tumor-infiltrating lymphocytes to knock out CISH should make them more responsive to the tumor antigens that they already recognize.
How Do You Build a Neoantigen-Reactive, Gene-Edited TIL Product?
The manufacturing pipeline is involved, and Dr. Johnson walked through it in stages:
- Resect and grow: Surgeons remove a tumor, often from a liver or lung metastasis. The tissue is cut into roughly two-millimeter cubes and cultured with high-dose interleukin-2 (IL-2) to expand the TIL inside.
- Find the neoantigens: Whole-exome sequencing and RNA sequencing of the tumor are compared against sequencing of the patient’s normal tissue to identify mutations that create candidate neoantigens.
- Test each fragment: Synthetic 25-amino-acid peptides carrying each mutation are presented to the patient’s own TIL cultures using the patient’s antigen-presenting cells. ELISpot and flow cytometry then show which TIL fragments react.
- Edit and expand: The reactive fragments are edited with CRISPR-Cas9 to knock out CISH, then grown over about two weeks in a rapid expansion protocol before infusion.
Across the trial, the team reached CISH knockout of roughly 70 to 90 percent in nearly every patient they attempted. The full process took on the order of 100 days, a timeline that mattered later.
What Happened in the Trial?
Here’s a breakdown of patient participation:
- 22 patients enrolled.
- TIL were collected from 20; nine patients withdrew before infusion, most because their disease progressed.
- 12 patients were dosed.
Among the 12 dosed patients, six (50%) had stable disease at 28 days and four (33%) had stable disease at 56 days. The side effects were the ones that the team expected (such as fatigue), and they traced to the lymphodepleting preconditioning regimen, the high-dose IL-2 given after infusion, or the underlying cancer, not to the edited cells. There were no severe cytokine release or neurotoxicity events.
One patient stood apart. A 34-year-old woman with microsatellite instability-high (MSI-H) colorectal cancer, refractory to standard chemotherapy and to anti-PD-1 and anti-CTLA-4 checkpoint inhibitors, had a complete response. Imaging showed the bulk of her tumor gone within a month and no measurable disease by roughly two months. Her response has continued beyond 28 months, and Dr. Johnson noted that it was approaching three years at the time of the talk.
What Did Immune Repertoire Sequencing Reveal About the Complete Response?
This is where immune repertoire sequencing earned its place. The team used deep TCR sequencing to read which T-cell clones sat in the infusion product and which appeared in the patient’s blood over time.
Because the infused cells carried a CISH knockout, the team could tell infusion-product TIL apart from the patient’s own T cells, something most TIL studies cannot do. Four days after infusion, about 80% of the T cells in her blood belonged to just 10 clones, and those clones matched the infusion product. They dropped off within about ten days.
Then two waves of new TCR clones appeared that had not been detectable before infusion or in the infusion product. The first started around day 10, the second around day 28. Dr. Johnson suggested this could reflect epitope spreading, in which the therapy triggers a broader endogenous immune response against the tumor.
Twenty-one clones from the infusion product persisted out to about 12 months. These persistent clones shared a distinct signature, with high expression of granzyme A (GZMA) along with RCBTB2, CXCR3, GBP5, and JAML, and notably low CISH. The low CISH is consistent with an origin in the edited product.
What Does This Mean for Precision Oncology and Cell Therapy?
The trial is a proof of concept. It shows that an intracellular checkpoint like CISH can be disrupted in a neoantigen-reactive cell product, that the product can be made safely, and that at least one patient can have a deep, durable response. Immuno-oncology has largely targeted checkpoints on the cell surface, so an intracellular target adds a genuinely different lever to the cancer immunotherapy toolkit.
Immune repertoire sequencing is a large part of why the result is legible. Tracking specific clones over a year turns a clinical outcome into mechanism, and it gives a way to ask which T cells actually drove the response.
Dr. Johnson was candid about the limits. Only one of the 12 dosed patients reached durable remission, so the therapy needs to become more potent. Additionally, the roughly 100-day manufacturing timeline was too slow for many patients, several of whom became ineligible as their disease advanced while the product was being made. Faster manufacturing and more potent TIL are the team’s priorities, along with identifying the neoantigens that the persistent and wave clones recognize.
For anyone working in precision oncology and cell therapy, this trial is a useful marker of where neoantigen-guided, gene-edited TIL therapy stands and what has to improve next.
If you’re interested in watching the full webinar, you can access it here.
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