Abstract 3143: Alternative splicing of CD19 mRNA in leukemias escaping CART-19 immunotherapy eliminates the cognate epitope and contributes to treatment failure
Authors: Sotillo Elena , Barrett David , Bagashev Aseb , Black Kathryn , Lanauze Caludia , Oldridge Derek , Sussman Robyn , Harrington Colleen , Chung Elaine Y. , Hofmann Ted J. , Maude Shannon L. , Martinez Nicole M. , Raman Pichai , Ruella Marco , Allman David , Jacoby Elad , Fry Terry , Barash Yoseph , Lynch Kristen W. , Mackall Crystal , Maris John , Grupp Stephen A. , Thomas-Tikhonenko Andrei 
Published: August 2015

Abstract
CD19 is expressed on most B-cell neoplasms, including acute lymphoblastic leukemias (B-ALL). Chimeric antigen receptor (CAR)-armed T cells targeting CD19 (CART-19) yield complete remission rate of 70-90% in B-ALL patients; the bispecific anti-CD19/CD3 antibody blinatumomab also shows clinical efficacy. Yet relapses due to the apparent CD19 loss have been observed following both therapies. Here we investigated the molecular mechanisms of epitope loss using five B-ALL samples obtained after CD19-directed therapy. These samples were matched, when available, with CD19-positive pre-treatment leukemias. Although the CD19 epitope recognized by CART-19 was undetectable in relapsed specimens, in all cases the CD19 genomic sequence was retained and the mRNA levels were only slightly reduced, suggesting regulation at the level of transcript processing. Indeed, using RT-PCR and RNA-Seq we detected several alternatively spliced CD19 mRNA species lacking exons 5-6 and/or exon 2 (Δex2), which encodes the cognate CART-19 epitope. In the sets of matched samples, the relative abundance of the Δex2/5-6 mRNA isoforms was increased post-treatment, and accordingly truncated CD19 protein variants were detectable using antibodies recognizing alternative epitopes. In one relapsed leukemia with a nonsense mutation in exon 2 of CD19, Δex2 was the only expressed isoform. To determine the contribution of alternative splicing to immune escape, we introduced CD19-expressing retroviruses into murine neoplastic B-cells, which had lost endogenous CD19 expression following silencing of its main transcriptional regulator Pax5. While skipping of exon 2 made the resultant protein invisible to CART-19, it partly rescued the defects in cell proliferation associated with CD19 loss. Collectively, these data suggest the existence of a novel mechanism of resistance to immunotherapy, based not on mutations in the coding sequence but rather on selection for alternatively spliced target protein isoforms (e.g., CD19 Δex2). Our findings could lead to the development of additional CD19-targeting CARTs for treating relapsed patients.
Citation Format: Elena Sotillo, David Barrett, Aseb Bagashev, Kathryn Black, Caludia Lanauze, Derek Oldridge, Robyn Sussman, Colleen Harrington, Elaine Y. Chung, Ted J. Hofmann, Shannon L. Maude, Nicole M. Martinez, Pichai Raman, Marco Ruella, David Allman, Elad Jacoby, Terry Fry, Yoseph Barash, Kristen W. Lynch, Crystal Mackall, John Maris, Stephen A. Grupp, Andrei Thomas-Tikhonenko. Alternative splicing of CD19 mRNA in leukemias escaping CART-19 immunotherapy eliminates the cognate epitope and contributes to treatment failure. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3143. doi:10.1158/1538-7445.AM2015-3143