A preclinical study published by Arnaud et al in Nature Biotechnology has demonstrated the utility and efficacy of a highly efficient method to generate large numbers of immune cells specifically engineered to recognize neoantigens and destroy the tumors that express them. Developed by a team of Ludwig Lausanne researchers led by investigators Alexandre Harari, PhD, and George Coukos, MD, PhD, the method, named NeoScreen, significantly improves the identification of a patient’s neoantigens and, according to the study authors, holds considerable promise for the development of personalized immunotherapies for cancer.
Study Background
“We wanted to develop a better way to both identify the neoantigens uniquely expressed by a patient’s tumors and efficiently isolate and expand the immune cells—tumor-infiltrating T cells—that are spontaneously directed against them, since it is these rare cells that are considered to be best at destroying cancer cells,” said Dr. Harari. “NeoScreen allows us to do all that. Better yet, it permits the identification of the specific receptors these T cells use to recognize neoantigens so that we can equip other T cells from a patient’s blood with that machinery and use those cells as well for personalized immunotherapy.”
To identify neoantigens and culture the T cells that detect them, researchers ordinarily isolate tumor-infiltrating lymphocytes from a tumor and grow them with that tumor’s constituent cells in the presence of immune factors that stimulate T-cell proliferation. But because neoantigen-specific tumor-infiltrating lymphocytes are very rare, the wholesale stimulation of T-cell growth often results in the far larger expansion of T cells that are not specifically targeted to neoantigens. This can drown out the most desirable neoantigen-targeting T cells in such cultures.
Methodology and Findings
To address this limitation, the investigators first modified the company in which isolated tumor-infiltrating lymphocytes are cultured, adding antigen-presenting cells into the mix. Antigen-presenting cells display antigens associated with disease to T cells and help drive the activation and proliferation of those that recognize the presented antigen. But instead of using typical antigen-presenting cells, like dendritic cells, the researchers engineered another type of immune cell, the B cell, to be a highly efficient antigen-presenting cell. B cells were considered ideal for this role because they are far more abundant in the blood and more amenable to genetic manipulation than dendritic cells.
The researchers then used computational methods to analyze the genome of tumor cells and identify randomly mutated parts of proteins that could be presented as neoantigens. Next, they pulsed the engineered B cells with those protein fragments—or inserted DNA encoding the fragments into the B cells—to get them to present the antigens. Finally, they cultured the B cells with tumor cells and the tumor-infiltrating lymphocytes isolated from that tumor.
Because antigen recognition stimulates T-cell proliferation, this coculture had the effect of selectively and rather dramatically expanding the tumor-infiltrating lymphocytes that recognize neoantigens expressed by the tumor. The researchers isolated those T cells, identified which of the neoantigens they recognized and sequenced the genes encoding their neoantigen-detecting T-cell receptors. This approach resulted in the identification of a far greater variety of both expressed neoantigens and T-cell receptors than did the conventional method.
The researchers showed that neoantigen-specific T-cell receptors could be cloned and inserted into other T cells taken from blood to generate large quantities of tumor-targeting T cells.
“NeoScreen enabled the selective expansion of neoantigen-targeting tumor-infiltrating lymphocytes against melanoma as well as colon, lung, and ovarian cancers,” said Dr. Coukos.
Finally, the researchers tested whether NeoScreen might be useful for adoptive T-cell therapy, in which T cells taken from a patient are isolated, selectively expanded, and reinfused into a patient. They show that T cells engineered to express T-cell receptors identified via NeoScreen recognized neoantigens found in tumors and could induce the regression of those same tumors after they were well established in a mouse model.
“NeoScreen could also be used to identify neoantigens for the design of personalized cancer vaccines for therapy,” said Dr. Coukos. “We will be testing this and other applications of NeoScreen for cancer immunotherapy at Ludwig Lausanne.”
Disclosure: This study was supported by Ludwig Cancer Research, the Swiss National Science Foundation, Cancera, Mats Paulssons, the Biltema Foundation, and the Centre Hospitalier Universitaire Vaudois (CHUV). For full disclosures of the study authors, visit www.nature.com.
