Fig. 6: Molecular analysis of CD123 loss following UCART123 treatment.

a RNA was isolated from 2 CD123⁺ samples from the vehicle-treated group (samples 1 and 2) and 4 CD123^- samples from the UCART123-treated group (samples 3, 5, 9 and 16). RT-PCR performed with primer pairs spanning the entire CD123 transcript detected full-length CD123 RNA (samples 1 and 2), truncated C123 RNA (sample 5), spliced CD123 isoforms (sample 16), or absence of CD123 mRNA (samples 3 and 9). Each RT-PCR experiment was repeated twice, on different dates, with essentially identical results. 100 bp DNA Ladders were used as molecular weight markers. Uncropped and unprocessed scans can be found in the Source Data file. b aGCH analysis performed on samples 3 (upper) and 9 (lower) showed a large genetic deletion on chromosome X, compared to CD123⁺ samples, corresponding to the location of CD123. c A Majiq-generated splice graph shows no exon junction reads for exons 9–12 of CD123 in sample 5. d Majiq-generated violin plots show the predominant splicing of exon 2 to exon 3 (red) in control (CD123 + ) samples but an increase in skipping from exon 2 to exon 5 (blue) in sample 16. The 95% confidence interval in this context is defined as follows: given observed reads in both experiments there is a 95% posterior probability that there is a change of 20% or more in percent-spliced-in (PSI). e A Majiq-generated splice graph shows increased skipping of exons 3–4 in sample 16 (lower panel) compared to control CD123⁺ samples (upper panel). Source data are provided as a Source data file.