Study reveals possible key to long-term survival among CAR T therapy patients

Chimeric antigen receptor (CAR) T therapy has proven to be highly effective in treating some blood cancers, with more than 90% of patients responding positively to the treatment. While some patients go into remission for more than a decade, though, more than half relapse within 12 months. The reason for the difference in patient outcomes is unclear. Now, researchers may know why - an advance that could significantly increase the number of long-term survivors.

A team of researchers led by Prof. Rong Fan at Yale University applied cutting-edge single-cell analysis technology to clinical trials initiated more than a decade ago. In doing so, they revealed what could be the driving force in CAR T therapy - which uses genetically engineered immune cells to attack cancer cells - to yield a very long-term complete remission. The results are published in Nature.  

For the study, the researchers used a method known as single-cell multi-omics established by Fan, the Harold Hodgkinson Professor of Biomedical Engineering and of Pathology and a member of Yale Cancer Center. Fan is a pioneer in this field and has been working on developing single-cell analysis techniques since 2006. It can capture the whole gene expression profile of each single CAR T cell from a patient. The researchers used it to sequence more than 1 million CAR T cells collected from 82 pediatric leukemia patients from two pioneering clinical trials launched in 2012 by Dr. Carl June at the University of Pennsylvania and Dr. Stephan Grupp at the Children’s Hospital of Philadelphia, who are co-senior authors in the Nature study. It is the largest single cell data set from the largest patient cohort in this field. 

Of those 82 patients, five had gone into remission for more than eight years. “The CAR T cells in these five patients demonstrate a very successful response,” said Zhiliang Bai, a postdoctoral associate in Fan’s lab and lead author of the study. “By comparing these CAR T cells to short-term and relapsed patients, we want to know what the molecular profile is, and what's the functional signature of these CAR T cells?” 

Their analysis found that the CAR T cells known as Type 2, widely known as immune-suppressive and associated with poor response in cancer immunotherapy, turned out to be a key player in inducing long-term remission. There are several categories of T cells, the most common being Type 1, which makes up about 20 percent of all T Cells. Type 2 cells make up only 3 percent but were found in much higher proportion in the patients with long remission times.  

Fan’s group conducted an earlier, smaller study that suggested the critical role of Type 2 CAR T cells. He and his collaborated then decided to expand on that study to find out why.  

“Because we have this large-scale data set, we can dissect the mechanisms,” Bai said. “The finding here is that the small population of Type 2 CAR T cells regulate and reduce T cell dysfunction to make the whole population of CAR T cells very healthy and persistent in the patients. This small population plays a critical role in regulating the hemostasis of all the cells. This is super exciting and unexpected to us.” 

Based on these results, the researchers collaborated with Dr. Li Tang of Swiss Federal Institute of Technology (EPFL) to conduct in vivo studies in which mice with leukemia were given CAR T cell therapy with a higher percentage of Type 2 cells, inducing a long-term remission in the mice. 

“This study demonstrated the power of large-scale single-cell multi-omics data from clinical trials that could precisely reveal how the therapy works in patients,” Fan said. “It also informs how to improve the design of CAR T cell therapy by harnessing Type 2 function as demonstrated in our paper by two different strategies. It provides valuable preclinical data for the next stage, which is potentially to conduct new trials that could lead to every patient being a long-term survivor.”

Grupp at Children’s Hospital of Philadelphia said the “intensely collaborative” project produced results that are “robust, comprehensive and impactful.” 

“Reverse engineering our most successful patient outcomes will potentially have life-saving implications for patients receiving CAR-T therapy,” he said.

June at Penn said the study could lead to significant improvements to the therapy.  

“We are excited that these new results point to a new bench to bedside approach to further improve CAR T therapy,” June said. 

Dr. Jos Melenhorst of Cleveland Clinic, a former member of Penn Medicine, also collaborated on and contributed significantly to the study.

Rong and Bai co-authored a second paper, also published in Nature, in which the researchers developed a therapy combining a type 2 protein, such as interleukin 4, with CAR T cells. Administered to mice with melanoma, breast cancer, and other solid tumors, the combination induced a longer-term remission in the mice. That paper was led by researchers from EPFL.