Finding the Underlying Mutations Driving CAR-T Failure

Researchers at Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine and Moffitt Cancer Center have used whole genome sequencing (WGS) to identify mutations that make B-cell lymphomas resistant to CAR-T immunotherapies. These findings highlight the importance of WGS to comprehensively map resistance mutations and chromosomal damage and could point to new interventions. The work was funded by a grant from the Florida Academic Center Alliance and published in the journal Blood.

“So much of the work in the field has focused on the tumor microenvironment and the overall inflammatory mechanisms that drive resistance,” said Associate Professor of Medicine and co-author Jonathan Schatz, M.D. “However, by looking at these genetic drivers together, we see how strongly they predict poor responses to CAR-T and possibly other therapies.”

CAR (chimeric antigen receptor) T cells are patient immune cells that have been engineered to target the CD19 receptor, which is commonly found on lymphoma and other cancer cells. These treatments have revolutionized care, in some cases producing long-term responses. However, some cancers develop resistance, making CAR-T immunotherapies ineffective in many patients.

The common wisdom has been that CAR-T resistance is primarily driven by obvious mechanisms. One is mutations in the CD19 receptor gene, which could weaken the engineered T cells’ ability to bind it. Another is the inflammatory tumor microenvironment, which protects cancers from immune cell incursions. In addition, immune cell exhaustion may virtually eliminate any response.

To better understand how these potential mechanisms may interact with the cancer’s genomic landscape, the researchers used WGS to read the genomes in 51 tumor samples from 49 patients. They found that a series of complex genomic variations laid the groundwork for cancers to resist CAR-T.

One culprit was APOBEC, an enzyme family that is often mutated in lymphoma, multiple myeloma, and other severe blood cancers. They also identified chromosomal deletions, including one that eliminates the tumor suppressor RHOA, and chromothripsis, in which chromosomes are radically rearranged. Surprisingly, the team did not find as many CD19 mutations as they expected.

“It really gets to this whole idea that there’s a complex interplay between tumors, immune environment and CAR-T cells,” said Dr. Schatz. “The same changes that made the tumor so aggressive in the first place are often keeping it from responding to immunotherapy.”

The study also highlights the importance of conducting whole genome sequencing, as opposed to exome sequencing, which only reads actual genes, leaving the vast majority of the genome invisible.

"Many of these alterations are widespread throughout the genome,” said Assistant Professor Francisco Maura, M.D., co-leader of the Myeloma Genomic Lab and co-author on the study. “If we base everything solely on the exome, we cannot see these complex events and ultimately ignore them. Whole genome is more expensive than exome sequencing, but it produces the data we need to get at cancer’s complexity.”

The authors believe these results, as well as follow-up research, will help make CAR-T and other cancer therapies more precise.

“By understanding the genomics behind cancer resistance, we gain new insights into patient care,” said Dr. Schatz. “We believe we can eventually develop an assay that will help identify the people who will or won’t respond to CAR-T and other treatments.”