Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy
Cancer discovery | 1 Nov 2015
E Sotillo, DM Barrett, KL Black, A Bagashev, D Oldridge, G Wu, R Sussman, C Lanauze, M Ruella, MR Gazzara, NM Martinez, CT Harrington, EY Chung, J Perazzelli, TJ Hofmann, SL Maude, P Raman, A Barrera, S Gill, SF Lacey, JJ Melenhorst, D Allman, E Jacoby, T Fry, C Mackall, Y Barash, KW Lynch, JM Maris, SA Grupp and A Thomas-Tikhonenko
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.
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