CRISPR Replaces Immune Receptors in Personalized Cancer Cell Therapy

A team led by scientists at PACT Pharma in South San Francisco and the University of California, Los Angeles (UCLA) have developed a method for isolating multiple T cell receptors (TCRs) from cancer patients for specific neoantigens and used a nonviral CRISPR editing approach to generate patient-specific neoTCRs in clinical-grade transgenic T cells for adoptive cell therapy (ACT) to treat cancer.

“This is a leap forward in developing a personalized treatment for cancer, where the isolation of immune receptors that specifically recognize mutations in the patient’s own cancer are used to treat the cancer,” said Antoni Ribas, MD, PhD, professor of medicine at UCLA’s Jonsson Comprehensive Cancer Center, and a senior author of the study. “The generation of a personalized cell treatment for cancer would not have been feasible without the newly developed ability to use the CRISPR technique to replace the immune receptors in clinical-grade cell preparations in a single step.”

In a first-in-human clinical trial (NCT03970382), researchers administered the new ACT in 16 patients with solid cancers (colon, breast, and lung cancers), with up to three unique lots of engineered T cells expressing neoTCRs targeting mutations on the patients’ cancer, following conditioning chemotherapy. The findings are published in the journal Nature.

Human TCRs on T cells can distinguish single point mutations in the cancer genome by detecting changes in the amino acid sequences of peptides presented by a range of human leucocyte antigens (HLA) that act as billboards on cell surfaces. Neoantigens are cancer-specific antigens generated by mutations in cancer cells. These neoantigens are the primary targets for an immune response and cancer therapies.

CRISPR editing has been used in humans earlier to remove specific genes to focus immune attacks on cancer cells. This is the first human study to describe an ACT that uses CRISPR to not only remove specific genes, but also to insert new ones in immune cells to redirect them to recognize mutations in the patient’s own cancer cells. When infused back into patients, CRISPR-engineered neoTCR-carrying T cells preferentially zero in on the patient’s cancer cells.

The technique used to isolate TCRs from the patient’s blood was developed initially through a collaboration of Ribas’ team with James Heath, PhD, president of the Institute for Systems Biology in Seattle, and the Nobel Laureate David Baltimore, PhD, emeritus professor at Caltech and member of the UCLA Jonsson Comprehensive Cancer Center. The technique was refined for clinical application by PACT Pharma. Upon isolation, the TCRs are used to redirect immune cells using CRISPR-based gene editing to recognize the patient’s own cancer cells.

“This study demonstrates the feasibility of isolating and cloning multiple immune cell receptors recognizing mutations in cancer cells, the simultaneous knock-out of the endogenous immune receptor and knock-in of the redirecting immune receptor using single-step, nonviral precision genome editing, the manufacturing of CRISPR engineered T cells at clinical grade, the safety of infusing up to three gene-edited immune cell products, and the ability of the gene-edited immune cells to traffic to the patients’ tumors,” said Ribas.

The study participants consented to provide a biopsy of the tumor and peripheral blood mononuclear cells (PBMC) to allow the investigators to screen for neoTCRs specific to the patients’ tumors.  The T cells were isolated from patient blood based on their binding to reagents that displayed up to 350 mutations from the patient’s own cancer, for a total of over 5,000 mutations being targeted across 34 HLA subtypes of the immune system.

The cancer-specific neoTCRs were then sequenced and inserted back into the patient’s own T cells using a one-step CRISPR editing method, which included the knock-out of two existing TCR genes (TCRα and TCRβ), and knock-in of the neoTCRs that could redirect T cells to recognize the patient’s own cancer cells.

Patients who received the new therapy experienced expected side effects from chemotherapy. Two of the 16 patients had potential side effects from the gene-edited cells but recovered promptly. Biopsy of the patient’s tumors following treatment showed that the edited cells constituted about 20% of the immune cells in the cancer.

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