Response to Bruton's tyrosine kinase inhibitors in aggressive lymphomas linked to chronic selective autophagy

We uncovered an autophagic pathway regulating survival in ABC DLBCL upon BTK inhibition using genome wide CRISPR screening. To investigate the mechanism of action of this unique form of autophagy, we performed RNA-seq on TMD8 cells knocked out for various ATG genes that either showed resistance to BTK inhibitors (ATG9A, ATG101, ATG14, RB1CC1, WIPI2), those that did not (ATG5, ATG7, ULK1 and 2 DKO, or non-targetingcontrol), or TMD8 cells knocked out for the known NF-kB negative regulator TNFAIP3. Cells were treated for 24 hours with the BTK inhibitor, acalabrutinib, and gene expression signatures were calculated from normalized RNA-seq reads. We found NF-kB gene expression signatures to be downregulated in control cells upon BTK inhibition, but not in ATG KO cells conferring BTK inhibitor resistance. Overall design: RNA sequencing was performed on TMD8 cells treated with vehicle (DMSO) or 25 nM acalabrutinib for 24 hours.