CD19-targeting CAR T cell immunotherapy outcomes correlate with genomic modification by vector integration
Christopher L. Nobles, Scott Sherrill-Mix, John K. Everett, Shantan Reddy, Joseph A. Fraietta, David L. Porter, Noelle Frey, Saar I. Gill, Stephan A. Grupp, Shannon L. Maude, Donald L. Siegel, Bruce L. Levine, Carl H. June, Simon F. Lacey, J. Joseph Melenhorst, Frederic D. Bushman
Christopher L. Nobles, Scott Sherrill-Mix, John K. Everett, Shantan Reddy, Joseph A. Fraietta, David L. Porter, Noelle Frey, Saar I. Gill, Stephan A. Grupp, Shannon L. Maude, Donald L. Siegel, Bruce L. Levine, Carl H. June, Simon F. Lacey, J. Joseph Melenhorst, Frederic D. Bushman
View: Text | PDF
Research Article Microbiology

CD19-targeting CAR T cell immunotherapy outcomes correlate with genomic modification by vector integration

Abstract

Chimeric antigen receptor–engineered T cells targeting CD19 (CART19) provide an effective treatment for pediatric acute lymphoblastic leukemia but are less effective for chronic lymphocytic leukemia (CLL), focusing attention on improving efficacy. CART19 harbor an engineered receptor, which is delivered through lentiviral vector integration, thereby marking cell lineages and modifying the cellular genome by insertional mutagenesis. We recently reported that vector integration within the host TET2 gene was associated with CLL remission. Here, we investigated clonal population structure and therapeutic outcomes in another 39 patients by high-throughput sequencing of vector-integration sites. Genes at integration sites enriched in responders were commonly found in cell-signaling and chromatin modification pathways, suggesting that insertional mutagenesis in these genes promoted therapeutic T cell proliferation. We also developed a multivariate model based on integration-site distributions and found that data from preinfusion products forecasted response in CLL successfully in discovery and validation cohorts and, in day 28 samples, reported responders to CLL therapy with high accuracy. These data clarify how insertional mutagenesis can modulate cell proliferation in CART19 therapy and how data on integration-site distributions can be linked to treatment outcomes.

Authors

Christopher L. Nobles, Scott Sherrill-Mix, John K. Everett, Shantan Reddy, Joseph A. Fraietta, David L. Porter, Noelle Frey, Saar I. Gill, Stephan A. Grupp, Shannon L. Maude, Donald L. Siegel, Bruce L. Levine, Carl H. June, Simon F. Lacey, J. Joseph Melenhorst, Frederic D. Bushman

×

Figure 6

Predicting clinical outcome from integration-site data.

Options: View larger image (or click on image) Download as PowerPoint
Predicting clinical outcome from integration-site data. A total of 91 fe...
A total of 91 features spanning population metrics, genomic features, and epigenetic features from 29 patients were used in LASSO logistic regression to build a classification model. Results are from leave-one-out cross-validation of models based on /preinfusion products (A) and day 28 peripheral blood samples (B). Bar plots indicate the contribution of different features to classification in each model. Positive values indicate correlation with a positive clinical outcome, while negative contributions indicate a correlation with negative clinical outcomes. (C) Vector integration in the CR/PRtd sample is favored in transcription units preferentially active in the T cells from CR/PRtd. RNA-Seq data were analyzed to identify the top 500 genes that were preferentially active in preinfusion products from CR/PRtd versus PR/NR. The frequency of integration in these genes (y axis) was then compared among integration sites from CR/PRtd versus PR/NR (x axis). Median values were compared using the Mann–Whitney U test.