Browsing by Author "Torres-Diz, Manuel"

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    High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance
    (2022) Cortés-López, Mariela; Schulz, Laura; Enculescu, Mihaela; Paret, Claudia; Spiekermann, Bea; Quesnel-Vallières, Mathieu; Torres-Diz, Manuel; Unic, Sebastian; Busch, Anke; Orekhova, Anna; Kuban, Monika; Mesitov, Mikhail; Mulorz, Miriam M.; Shraim, Rawan; Kielisch, Fridolin; Faber, Jörg; Barash, Yoseph; Thomas-Tikhonenko, Andrei; Zarnack, Kathi; Legewie, Stefan; König, Julian
    Following CART-19 immunotherapy for B-cell acute lymphoblastic leukaemia (B-ALL), many patients relapse due to loss of the cognate CD19 epitope. Since epitope loss can be caused by aberrant CD19 exon 2 processing, we herein investigate the regulatory code that controls CD19 splicing. We combine high-throughput mutagenesis with mathematical modelling to quantitatively disentangle the effects of all mutations in the region comprising CD19 exons 1-3. Thereupon, we identify ~200 single point mutations that alter CD19 splicing and thus could predispose B-ALL patients to developing CART-19 resistance. Furthermore, we report almost 100 previously unknown splice isoforms that emerge from cryptic splice sites and likely encode non-functional CD19 proteins. We further identify cis-regulatory elements and trans-acting RNA-binding proteins that control CD19 splicing (e.g., PTBP1 and SF3B4) and validate that loss of these factors leads to pervasive CD19 mis-splicing. Our dataset represents a comprehensive resource for identifying predictive biomarkers for CART-19 therapy.