Study Identifies Splicing Alterations That Enable Resistance to CD19 CAR T-Cell Immunotherapy
Although the CD19 antigen expressed on most B-cell acute lymphoblastic leukemias (ALL) can be targeted with chimeric antigen receptor–armed T cells (CART-19), relapse rates among pediatric and adult patients with the cancer remain high. In this study by Sotillo et al, the researchers investigated the clinical issue of resistance to CD19 CAR T-cell immunotherapy in pediatric patients with B-cell ALL. They found that the resistance can be caused by CD19 splicing alterations, which result in the loss of certain parts of the CD19 protein that are recognized by the CAR T cells. Targeting alternative CD19 ectodomains may improve survival of patients with B-cell neoplasms, according to the study abstract. The study is published in Cancer Discovery.
Study Methodology
Using a variety of sequencing methods, including whole-exome and RNA sequencing, as well as copy-number alteration analysis, the investigators examined multiple tumor samples from four pediatric patients with B-cell acute lymphoblastic leukemia collected before they were treated with CD19 CAR T-cell therapy and/or after they developed resistance to the therapy.
Study Findings
The researchers found that in some cases, one of the two copies of the gene coding for CD19 and located on chromosome 16 was deleted, and the other copy was damaged as a result of mutations in coding areas of the CD19 gene, usually in exon 2. They also found through the process of alternative splicing that in the same cases exons 2, 5, and 6 were frequently skipped, making mutations in exon 2 largely irrelevant.
In a series of experiments to learn the impact gene splicing might have on the production of CD19 protein, the researchers found that the deletion of exons 5 and 6 resulted in premature termination of the protein and that the deletion of exon 2 resulted in the production of a modified version of CD19, which was more stable than its standard version. They also found that the shortened protein was functional and could perform many of the tasks that CD19 is known to handle.
Study Significance
CART-19 therapy yields 70% response rates in patients with B-cell ALL but also produces “escape variants,” concluded the researchers. “We discovered that the underlying mechanism is the selection for preexisting alternatively spliced CD19 isoforms with the compromised CART-19 epitope. This mechanism suggests a possibility of targeting alternative CD19 ectodomains, which could improve survival of patients with B-cell neoplasms.”
Andrei Thomas-Tikhonenko, PhD, of The Children’s Hospital of Philadelphia, University of Pennsylvania, is the corresponding author of the Cancer Discovery study.
Funding for this study was provided by V Foundation for Cancer Research, William Lawrence and Blanche-Hughes Foundation, Leukemia & Lymphoma Society, Alex’s Lemonade Stand Foundation, the National Institutes of Health, and Stand Up to Cancer-St. Baldrick’s Pediatric Dream Team Translational Research Grant. For full disclosures of the study authors, visit cancerdiscovery.aacrjournals.org.
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