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Cancer Discov. 2015 Dec;5(12):1282-95. doi: 10.1158/2159-8290.CD-15-1020. Epub 2015 Oct 29.

Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy.

Author information

1
Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
2
Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
3
Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania. Immunology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
4
Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania. Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
5
Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
6
Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania. Department of Biochemistry & Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
7
Department of Biochemistry & Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
8
Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania. Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
9
Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
10
Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania. Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
11
Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
12
Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
13
Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland.
14
Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania. Immunology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania. Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania. Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania. andreit@mail.med.upenn.edu.

Abstract

The CD19 antigen, expressed on most B-cell acute lymphoblastic leukemias (B-ALL), can be targeted with chimeric antigen receptor-armed T cells (CART-19), but relapses with epitope loss occur in 10% to 20% of pediatric responders. We detected hemizygous deletions spanning the CD19 locus and de novo frameshift and missense mutations in exon 2 of CD19 in some relapse samples. However, we also discovered alternatively spliced CD19 mRNA species, including one lacking exon 2. Pull-down/siRNA experiments identified SRSF3 as a splicing factor involved in exon 2 retention, and its levels were lower in relapsed B-ALL. Using genome editing, we demonstrated that exon 2 skipping bypasses exon 2 mutations in B-ALL cells and allows expression of the N-terminally truncated CD19 variant, which fails to trigger killing by CART-19 but partly rescues defects associated with CD19 loss. Thus, this mechanism of resistance is based on a combination of deleterious mutations and ensuing selection for alternatively spliced RNA isoforms.

SIGNIFICANCE:

CART-19 yield 70% response rates in patients with B-ALL, but also produce escape variants. 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.

PMID:
26516065
PMCID:
PMC4670800
DOI:
10.1158/2159-8290.CD-15-1020
[Indexed for MEDLINE]
Free PMC Article

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