CARD11 gain of function upregulates BCL2A1 and promotes resistance to targeted therapies combination in B-cell lymphoma

Strategy combining targeted therapies is effective in B-cell lymphomas such as mantle cell lymphoma (MCL), but acquired resistances remain a recurrent issue. Herein, we performed integrative longitudinal genomic and single-cell RNA-seq analyses of MCL patients treated with targeted therapies against CD20, BCL2 and BTK (i.e., OAsIs trial). We revealed the emergence of subclones with a selective advantage against OAsIs combination in vivo and showed that resistant cells were characterized by BCR-independent overexpression of NFkB1 target genes, especially due to CARD11 mutations. Functional studies demonstrated that CARD11 gain of function not only resulted in BCR independence, but also directly increase the transcription of the antiapoptotic BCL2A1, leading to venetoclax and OAsIs combination resistance. Based on the transcriptional profile of OAsIs-resistant subclones, we designed a 16-gene resistance signature that was also predictive for MCL patients treated with conventional chemotherapy, underlying a common escape mechanism. Among druggable strategies to inhibit CARD11-dependent NFkB1 transduction, we evaluated the selective inhibition of its essential partner MALT1. We demonstrated that MALT1 protease inhibition led to the reduction of genes involved in OAsIs resistance, including BCL2A1. Consequently, MALT1 inhibition induced synergistic cell death in combination with BCL2 inhibition, irrespective of CARD11 mutational status, both in vitro and in vivo. Taken together our study identified mechanisms of resistance to targeted therapies and provided a novel strategy to overcome resistance in aggressive B-cell lymphoma.